Lysm receptor-like kinases to improve plant defense response against fungal pathogens

ABSTRACT

Perception of chitin fragments (chitooligosaccharides) is an important first step in plant defense response against fungal pathogen. LysM receptor-like kinases (LysM RLKs) are instrumental in this perception process. LysM RLKs also play a role in activating transcription of chitin-responsive genes (CRGs) in plants. Mutations in the LysM kinase receptor genes or the downstream CRGs may affect the fungal susceptibility of a plant. Mutations in LysM RLKs or transgenes carrying the same may be beneficial in imparting resistance against fungal pathogens.

This application is a divisional application of pending U.S. patentapplication Ser. No. 13/347,199 filed Jan. 10, 2012, which is adivisional application of U.S. patent application Ser. No. 11/835,328filed Aug. 7, 2007, which claims priority to U.S. provisional patentapplication Ser. No. 60/836,084 filed on Aug. 7, 2006. All of theaforementioned applications are incorporated herein by reference intothis application.

GOVERNMENT INTERESTS

This work was funded in part by a grant from the United StatesDepartment of Energy, Energy Biosciences Program, Office of Basic EnergySciences (grant number DE-FG02-02ER15309). The United States governmentmay have certain rights in the invention disclosed herein.

SEQUENCE LISTING

This application is accompanied by a sequence listing that accuratelyreproduces the sequences described herein.

BACKGROUND

This disclosure relates to the use of molecular genetic technologyinvolving LysM receptor kinase family genes and the expression ornonexpression thereof to modulate plant defense responses, especiallyagainst fungal pathogens.

Fungal disease causes significant agricultural losses in the UnitedStates and other parts of the world. Control of these pathogens isparticularly difficult, often requiring treatment of entire fields withbiocidal compounds. Although effective, increasing concern about theenvironmental and economic costs of such treatments require the need foralternative control methods.

Phakopsora pachyrhizi is a fungus that causes a rust disease of soybean(Glycine max), also known as Asian Soybean Rust. The pathogen has spreadfrom Asia to all other soybean production regions in the world, and isreported to have arrived in the United States in the fall of 2004. Atpresent, there is no known durable resistance available in any soybeanvarieties. Uromyces appendiculatus is a fungus that causes rust on bean(Phaseolus vulgaris). Breeders are working to identify genes in beanthat can be manipulated for rust resistance. United States soybeanproducers have anticipated the arrival of P. pachyrhizi, the fungus thatcauses soybean rust, since its reported occurrence in Brazil. Thearrival of P. pachyrhizi in the U.S. in late 2004 ended theanticipation, and farmers must now respond to the potential annualoccurrence of this new disease. Farmer concerns have been based onreports of losses ranging from 10 to 80% in other regions of the worldwhen control measures were not successfully implemented.

As rust-inducing fungi, U. appendiculatus and P. pachyrhizi belong tothe order Uredinales, within the class Basidiomycetes. U. appendiculatusproduces five spore stages on a single host plant. P. pachyrhizireproduces predominantly by uredospores on a single host plant.Uredospores are responsible for rapid spread of the fungus. P.pachyrhizi can infect dozens of legume species, in addition to soybean.

Uredospores of U. appendiculatus penetrate through foliar stomatalopenings. P. pachyrhizi differs in that germinated uredospores penetratedirectly through the leaf epidermal cell layer. Typically, a uredosporethat lands on a leaf surface germinates to produce an infection pad(appressorium) that adheres to the surface. In both species, theappressorium produces a hyphal peg that penetrates the plant. Afterpenetration, each fungus develops thread-like structures (hyphae) thatgrow inter-cellularly through leaf tissues. The hyphae enter host cellswithout killing them. There, they produce spherical structures(haustoria) that extract nutrients from the living leaf cells. Soonafter infection each fungus forms uredia that produce additional spores.

Soybean producers are particularly concerned because no durable, naturalresistance to rust has been discovered after testing more than 18,000soybean varieties. The pathogen, P. pachyrhizi can potentially infectany cultivar produced. In anticipation of the arrival of the rustpathogen, a great deal of research has been conducted to identifyeffective fungicides, and emergency governmental clearance forapplication to soybean has been obtained. Traditional screening andbreeding methods have identified no major resistance genes to theaforementioned pathogens, and particularly in the case of U.appendiculatus and P. pachyrhizi.

Fungicides will likely be the front-line of defense against these andother fungal pathogens for many years until new resistance genes orother forms of resistance are identified. Fungicides have nottraditionally been used in most soybean production. Consequently, thereis limited information concerning the costs of this disease managementpractice and its likely economic viability. Widespread use of fungicidesmay also raise environmental concerns. These concerns have led tovariable estimates of the acreage in Missouri and other states that maybe shifted from soybean to alternative crops.

To protect soybean farmers and to ensure that soybean production meetsincreasing market demand, it is imperative that alternatives tofungicides be developed as rapidly as possible. Biotechnology-basedapproaches for defense against plant diseases are more preferable due tothe minimal use of chemicals and the relative ease of deployment.

Chitin is a polymer of N-acetyl-D-glucosamine, found in fungal cellwalls, insect exoskeletons, and crustacean shells. It has beenhypothesized that plant chitinases can degrade chitin in the fungal cellwalls to directly affect the viability of the invading fungal pathogenand to release short fragments (chitooligosaccharides) that can act as ageneral elicitor of plant innate immunity pathways. See e.g., Shibuya etal., 2001 and Stacey et al., 1997. In support of the above hypothesis,purified chitooligosaccharides have been shown to induce various defenseresponses in plants or cultured cells, such as induction of defenserelated genes and synthesis of phytoalexin. Shibuya et al., 2001 andRamonell et al., 2005.

More particularly, chitooligosaccharides have been shown to induce alarge number of genes (including many defense-related genes), andmutations in selected chitooligosaccharide-responsive genes orchitin-responsive genes (CRGs) have been shown to increase thesusceptibility of a plant to certain fungal pathogens. See Ramonell etal., 2002; and Ramonell et al., 2005. Taken together, these studiessuggest that plants possess a specific system to recognizechitooligosaccharides which, in turn, activate defense genes. Seegenerally, Day et al., 2001; Zhang et al., 2002; Wan et al., 2004; Kakuet al., 2006; and Libault et al., 2007.

Previous work has reported chitin recognition in rice and legumes.Stacey, G. and N. Shibuya, Plant and Soil 194: 161-169 (1997) Theability of Arabidopsis thaliana to recognize and respond to chitin hasalso been reported. A variety of genes have been shown to respond tochitin treatment. See e.g., Ramonell et al. Microarray analysis ofchitin elicitation in Arabidopsis thaliana. Mol. Plant Pathol. 3 (1):301-311 (2002) and Zhang et al., Characterization of Early,Chitin-Induced Gene Expression in Arabidopsis Mol. Plant-Microbe Int.15: 963-970 (2002) and Wan et al., Activation of a potentialmitogen-activated protein kinase pathway in Arabidopsis by chitin. Mol.Plant Pathol. 5(1): 125-135 (2004).

More specifically, chitin binding sites or proteins have been previouslyidentified in membrane preparations of a variety of plant cells. Day etal., 2001; Ito et al., 1997; and Okada et al, 2002. More recently, aLysM domain-containing protein (CEBiP) has been shown to be involved inthe binding and recognition of chitooligosaccharides in rice. Kaku etal., 2006. The LysM motif was originally identified in bacterial enzymesthat degrade cell wall component peptidoglycan, which is structurallysimilar to chitin. Joris, 1992. Since CEBiP lacks a significantintracellular domain, it likely functions as part of a chitin receptorcomplex. Kaku et al., 2006. However, no such chitin receptor complexeshave been identified.

SUMMARY

The present disclosure overcomes the problems outlined above andadvances the art by providing methods to confer fungal resistance toplants. This disclosure addresses a new biotechnology-based approach togenerate rust resistant soybean and to confer rust resistance uponsoybean plants. The technology also involves the development and/ordeployment of defense peptides against fungal pathogen, such as theAsian soybean rust fungus. The technology similarly applies to otherpathogens in plants, such as the field bean (Phaseolus vulgaris) rustpathogen, Uromyces appendiculatus.

It is hereby disclosed a number of LysM-containing receptor like kinases(“LysM RLKs”) in soybean, as well as in other legume or non-legumeplants. The lysine motif (LysM) domain is an ancient and ubiquitousprotein module that binds peptidoglycan and structurally relatedmolecules. A genomic survey in a large number of species spanning allkingdoms reveals that the combination of LysM and receptor kinasedomains is present exclusively in plants. Table 1 lists a number ofgenes encoding LysM containing proteins from both prokaryotes andeukaryotes, along with their accession numbers from GenBank or otherdatabases.

TABLE 1 LysM family genes in prokaryotes and eukaryotes LysM motifkingdom domain species name sources accession number >AGRT52b BacteriaProteobacteria alpha- Argobacterium_tumefaciens_C58 UniProt/TrEMBLQ8UEQ5 proteobacteria >ANASP1 Bacteria Cyanobacteria Nostoc_PCCUniProt/TrEMBL Q8YRU0 >BACAN1a Bacteria Firmicutes Bacillus_anthracisUniProt/TrEMBL Q81WS5 >BACAN2b Bacteria Firmicutes Bacillus_anthracisUniProt/TrEMBL Q81Y89 >BACAN7 Bacteria Firmicutes Bacillus_anthracisUniProt/TrEMBL Q81SZ3 >BORPE5 Bacteria Proteobacteria Beta-bordetella_pertussis UniProt/TrEMBL Q7W0R5 proteobacteria >BORPE6Bacteria Proteobacteria Beta- bordetella_pertussis UniProt/TrEMBL Q7VY72proteobacteria >BRAJA1 Bacteria Proteobacteria alpha-Bradyrhizobium_japonicum UniProt/TrEMBL Q89Y08 proteobacteria >BRAJA2Bacteria Proteobacteria alpha- Bradyrhizobium_japonicum UniProt/TrEMBLQ89XF2 proteobacteria >BURPS1 Bacteria Proteobacteria Beta-Burkholderia_pasudomallei_1710b UniProt/TrEMBL Q63LR7proteobacteria >BURPS4 Bacteria Proteobacteria Beta-Burkholderia_pasudomallei_1710b UniProt/TrEMBL Q63TI4proteobacteria >BURPS6a Bacteria Proteobacteria Beta-Burkholderia_pasudomallei_1710b UniProt/TrEMBL Q63V96proteobacteria >CHLAU2 Bacteria Chloroflexi Chloroflexus_aurantiacusUniProt/TrEMBL Q3E5J5 >ECOLI6 Bacteria Proteobacteria Gama-Escherichia_coli UniProt/TrEMBL P75954 proteobacteria >PELCD5a BacteriaProteobacteria Delta- Pelobacter_carbinolicus_DSM UniProt/TrEMBL Q3A2X4proteobacteria >RALSO3 Bacteria Proteobacteria Beta-Ralstonia_solanacearum UniProt/TrEMBL Q8Y0H0 proteobacteria >RALSO6Bacteria Proteobacteria Beta- Ralstonia_solanacearum UniProt/TrEMBLQ8XZ88 proteobacteria >RHOPA4 Bacteria Proteobacteria Alpha-Rhodopseudomonas_palustris UniProt/TrEMBL Q379H8 proteobacteria >SALCH2Bacteria Proteobacteria Gama- Salmonella_choleraesuis UniProt/TrEMBLQ5J4C2 proteobacteria >SALCH5 Bacteria Proteobacteria Gama-Salmonella_choleraesuis UniProt/TrEMBL Q57QE0 proteobacteria >STRCO4Bacteria Firmicutes Actinobacteridae Streptomyces_coelicolorUniProt/TrEMBL Q9ACX5 >VIBCH4 Bacteria Proteobacteria Gama-Vibrio_cholerae UniProt/TrEMBL Q9KNA7 proteobacteria >VIBCH5a BacteriaProteobacteria Gama- Vibrio_cholerae UniProt/TrEMBL Q9KV14proteobacteria >WOLSU1a Bacteria Proteobacteria Epsilon-wolinella_succinogenes UniProt/TrEMBL Q7M7V0 proteobacteria >WOLSU1bBacteria Proteobacteria Epsilon- wolinella_succinogenes UniProt/TrEMBLQ7M7V0 proteobacteria >CAEEL1 Eukaryota Metazoa NematodaCaenorhabditis_elegans UniProt/TrEMBL P90882 >CAEEL6 Eukaryota MetazoaNematoda Caenorhabditis_elegans UniProt/TrEMBL Q93715 >CHLRE1 EukaryotaChlorophyta Chlamydomonas_reinhardtii UniProt/TrEMBL Q9M5B9 >DICDI2Eukaryota Mycetozoa Dictyosteliida Dictyostelium_discoideumUniProt/TrEMBL Q54BF7 >DROME10 Eukaryota Metazoa ChordataDrosophila_melanoqaster UniProt/TrEMBL Q9V4P7 >DROME9 Eukaryota MetazoaChordata Drosophila_melanoqaster UniProt/TrEMBL Q9VNA1 >HUMAN1 EukaryotaMetazoa Chordata Homo_sapiens UniProt/TrEMBL Q5TF95 >HUMAN7 EukaryotaMetazoa Chordata Homo_sapiens UniProt/TrEMBL Q7Z3D4 >MOUSE5 EukaryotaMetazoa Chordata Mus_musculus UniProt/TrEMBL Q99LE3 >MOUSE9 EukaryotaMetazoa Chordata Mus_musculus UniProt/TrEMBL Q6DFV7 >XENLA5 EukaryotaMetazoa Chordata Xenopus_laevis UniProt/TrEMBL Q5BJ38 >AtLYK1b EukaryotaViridiplantae Streptophyta Arabidopsis_thaliana TAIR At2g21630 >AtLYK1cEukaryota Viridiplantae Streptophyta Arabidopsis_thaliana TAIRAt2g21630 >AtLYK2 Eukaryota Viridiplantae StreptophytaArabidopsis_thaliana TAIR At3g01840 >AtLYK3 Eukaryota ViridiplantaeStreptophyta Arabidopsis_thaliana TAIR At1g51940 >AtLYK4a EukaryotaViridiplantae Streptophyta Arabidopsis_thaliana TAIR At2g23770 >AtLYK4bEukaryota Viridiplantae Streptophyta Arabidopsis_thaliana TAIRAt2g23770 >AtLYK4c Eukaryota Viridiplantae StreptophytaArabidopsis_thaliana TAIR At2g23770 >AtLYK5a Eukaryota ViridiplantaeStreptophyta Arabidopsis_thaliana TAIR At2g33580 >AtLYK5c EukaryotaViridiplantae Streptophyta Arabidopsis_thaliana TAIR At2g33580 >AtLYP1bEukaryota Viridiplantae Streptophyta Arabidopsis_thaliana TAIRAt1g21880 >AtLYP2a Eukaryota Viridiplantae StreptophytaArabidopsis_thaliana TAIR At1g77630 >AtLYP3a Eukaryota ViridiplantaeStreptophyta Arabidopsis_thaliana TAIR At2g17120 >AtLYP3b EukaryotaViridiplantae Streptophyta Arabidopsis_thaliana TAIR At2g17120 >AtLysMe1Eukaryota Viridiplantae Streptophyta Arabidopsis_thaliana TAIRAt3g52790 >AtLysMe2 Eukaryota Viridiplantae StreptophytaArabidopsis_thaliana TAIR At4g25433 >AtLysMe3 Eukaryota ViridiplantaeStreptophyta Arabidopsis_thaliana TAIR At5g62150 >AtLysMn1 EukaryotaViridiplantae Streptophyta Arabidopsis_thaliana TAIR At1g55000 >AtLysMn2Eukaryota Viridiplantae Streptophyta Arabidopsis_thaliana TAIRAt5g08200 >AtLysMn3 Eukaryota Viridiplantae StreptophytaArabidopsis_thaliana TAIR At5g23130 >GmLYK10b Eukaryota ViridiplantaeStreptophyta Glycine_max this study GmW2080D08.12 >GmLYK10c EukaryotaViridiplantae Streptophyta Glycine_max this study GmW2080D08.12 >GmLYK11Eukaryota Viridiplantae Streptophyta Glycine_max this studyGmW2042I24.15 >GmLYK2 Eukaryota Viridiplantae Streptophyta Glycine_maxthis study GmW2098N11.15 >GmLYK4b Eukaryota Viridiplantae StreptophytaGlycine_max this study GmW2095P01.22 >GmLYK4c Eukaryota ViridiplantaeStreptophyta Glycine_max this study GmW2095P01.22 >GmLYK8a EukaryotaViridiplantae Streptophyta Glycine_max this study GmW2098N11.2 >GmLYK8bEukaryota Viridiplantae Streptophyta Glycine_max this studyGmW2098N11.2 >GmLYK9b Eukaryota Viridiplantae Streptophyta Glycine_maxthis study GmW2069O12.22 >GmLYK9c Eukaryota Viridiplantae StreptophytaGlycine_max this study GmW2069O12.22 >GmLYP1b Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLYP2a Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLYP2b Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLYP3a Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLYP3b Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLysMe1 Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLysMe2 Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLysMe3 Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLysMe4 Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLysMn1 Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLysMn2 Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmLysMn3 Eukaryota ViridiplantaeStreptophyta Glycine_max TIGR >GmNFR1ab Eukaryota ViridiplantaeStreptophyta Glycine_max this study >GmNFR1ac Eukaryota ViridiplantaeStreptophyta Glycine_max this study >GmNFR5aa Eukaryota ViridiplantaeStreptophyta Glycine_max this study >GmNFR5ab Eukaryota ViridiplantaeStreptophyta Glycine_max this study >GmNFR5ac Eukaryota ViridiplantaeStreptophyta Glycine_max this study >MtLYK10a Eukaryota ViridiplantaeStreptophyta Medicago_truncatula Medicago truncatula AC148994_13sequencing resources >MtLYK10b Eukaryota Viridiplantae StreptophytaMedicago_truncatula Medicago truncatula AC148994_13 sequencingresources >MtLYK10c Eukaryota Viridiplantae StreptophytaMedicago_truncatula Medicago truncatula AC148994_13 sequencingresources >MtLYK12b Eukaryota Viridiplantae StreptophytaMedicago_truncatula Medicago truncatula AC126779_3 sequencingresources >MtLYK12c Eukaryota Viridiplantae StreptophytaMedicago_truncatula Medicago truncatula AC126779_3 sequencingresources >MtLYK13a Eukaryota Viridiplantae StreptophytaMedicago_truncatula Medicago truncatula AC126779_4 sequencingresources >MtLYK13b Eukaryota Viridiplantae StreptophytaMedicago_truncatula Medicago truncatula AC126779_4 sequencingresources >MtLYK3b Eukaryota Viridiplantae StreptophytaMedicago_truncatula Gene Bank AY372402 >MtLYK3c Eukaryota ViridiplantaeStreptophyta Medicago_truncatula Gene Bank AY372402 >MtLYK9a EukaryotaViridiplantae Streptophyta Medicago_truncatula Medicago truncatulaAC148241_11 sequencing resources >MtLYK9b Eukaryota ViridiplantaeStreptophyta Medicago_truncatula Medicago truncatula AC148241_11sequencing resources >MtLYK9c Eukaryota Viridiplantae StreptophytaMedicago_truncatula Medicago truncatula AC148241_11 sequencingresources >OsLYK2b Eukaryota Viridiplantae Streptophyta Oryza_sativaTIGR LOC_Os06g41980 >OsLYK2c Eukaryota Viridiplantae StreptophytaOryza_sativa TIGR LOC_Os06g41980 >OsLYK3 Eukaryota ViridiplantaeStreptophyta Oryza_sativa TIGR LOC_Os06g41960 >OsLYK4b EukaryotaViridiplantae Streptophyta Oryza_sativa TIGR LOC_Os02g09960 >OsLYK4cEukaryota Viridiplantae Streptophyta Oryza_sativa TIGRLOC_Os02g09960 >OsLYK5a Eukaryota Viridiplantae StreptophytaOryza_sativa TIGR LOC_Os03g13080 >OsLYK5c Eukaryota ViridiplantaeStreptophyta Oryza_sativa TIGR LOC_Os03g13080 >OsLYK6a EukaryotaViridiplantae Streptophyta Oryza_sativa TIGR LOC_Os11g35330 >OsLYK6bEukaryota Viridiplantae Streptophyta Oryza_sativa TIGRLOC_Os11g35330 >OsLYK6c Eukaryota Viridiplantae StreptophytaOryza_sativa TIGR LOC_Os11g35330 >OsLYP1b Eukaryota ViridiplantaeStreptophyta Oryza_sativa TIGR LOC_Os03g04110 >OsLYP2a EukaryotaViridiplantae Streptophyta Oryza_sativa TIGR LOC_Os09g37600 >OsLYP2bEukaryota Viridiplantae Streptophyta Oryza_sativa TIGRLOC_Os09g37600 >OsLYP3a Eukaryota Viridiplantae StreptophytaOryza_sativa TIGR LOC_Os06g10660 >OsLYP3b Eukaryota ViridiplantaeStreptophyta Oryza_sativa TIGR LOC_Os06g10660 >OsLYP5b EukaryotaViridiplantae Streptophyta Oryza_sativa TIGR LOC_Os02g53000 >OsLYP6aEukaryota Viridiplantae Streptophyta Oryza_sativa TIGRLOC_Os11g34570 >OsLYP6b Eukaryota Viridiplantae StreptophytaOryza_sativa TIGR LOC_Os11g34570 >OsLysMe1 Eukaryota ViridiplantaeStreptophyta Oryza_sativa TIGR LOC_Os01g57390 >osLysMe2 EukaryotaViridiplantae Streptophyta Oryza_sativa TIGR LOC_Os01g57400 >OsLysMe3Eukaryota Viridiplantae Streptophyta Oryza_sativa TIGRLOC_Os04g48380 >OsLysMn1 Eukaryota Viridiplantae StreptophytaOryza_sativa TIGR LOC_Os03g49250 >OsLysMn2 Eukaryota ViridiplantaeStreptophyta Oryza_sativa TIGR LOC_Os06g51360 >PtLysMe4 EukaryotaViridiplantae Streptophyta Populus_trichocarpa DOE JGIEUGENE3.00051310 >PtLysMe8 Eukaryota Viridiplantae StreptophytaPopulus_trichocarpa DOE JGI EUGENE3.00070396 >PtLysMe9 EukaryotaViridiplantae Streptophyta Populus_trichocarpa DOE JGIEUGENE3.00110096 >PtLysMe11 Eukaryota Viridiplantae StreptophytaPopulus_trichocarpa DOE JGI EUGENE3.00070285

In comparison to the LysM proteins in other kingdoms, plant LYK proteinspossess unique features: (1) the combination of LysM and kinase domainsexists exclusively in the plant lineage; (2) plant LYK proteins have nomore than three LysM motifs; (3) if more than two LysM motifs existwithin a single plant LYK protein, they are always distinct from eachother at the protein sequence level; and (4) the LysM domain sequencesin plant LYK proteins are highly diversified due to differentcombinations of heterogenous LysM motifs. Based on the sequencephylogenies, LysM motifs (named LYKa, LYKb, and LYKc from the N to the Cterminus) in plant LYK proteins largely fall into five clades (FIG. 1A).This distribution of LysM motifs was found in all six plant speciesstudied (i.e. LysM motifs from dicots and rice are clustered together ineach Glade, suggesting that the diversification event of plant LysMmotifs predated the divergence of monocot and dicot plants).

The LysM motifs from non-kinase plant LysM proteins have also beeninvestigated. These sequences have been retrieved using BLAST searchesagainst genomic sequence databases of Arabidopsis, rice, and poplar andEST sequences of soybean. Based on their subcellular localizationpredictions and domain arrangements, non-kinase plant LysM proteins maybe further categorized into three subgroups, including LysM-typereceptor-like proteins (LYPs), extracellular LysM proteins (LysMe), andnonsecretory intracellular LysM proteins (LysMn; FIG. 1B). This groupingwill be helpful in understanding the nature of each LysM protein andproviding insightful clues to the biological functions.

FIG. 1B illustrates the general domain structure of different LysMcontaining proteins. As shown in FIG. 1B, LysM RLKs (also referred to as“LYK”) typically possess one or more LysM domains, a transmembranedomain and a kinase domain. The LysM domain is known for its capabilityto bind chitin. The transmembrane domain may serve to anchor the LysMRLKs in the membrane of the cells, whereas the kinase domain extendsinto the cytoplasm where it may phosphorylate specific substrates in thecell. In one embodiment, it is conceivable that the transmembrane domainof an LYK may be replaced with a different transmembrane domain fromanother LYK, or from another transmembrane protein,

As shown in FIG. 1 and FIG. 2, LysM domains in plants are highlydiversified and that at least six distinct types of LysM motifs exist inplant LysM kinase proteins, which are shown as Types I-V and VII in FIG.1B. Five additional types of LysM motifs exist in non-kinase plant LysMproteins, designated as Types VI, VIII-XI as shown in FIG. 1B. See alsoZhang et al., Plant Physiol. 144, 623-636 (2007), which is herebyexpressly incorporated by reference. FIG. 2 shows sequence alignment ofrepresentative LysM domains. FIG. 2A shows an alignment of 93LysM-containing proteins in plants. Shaded areas indicate conservedresidues in FIG. 2. FIG. 2B is an alignment of LysM domains from the LYKGroup I, which contains LysM motif Types II and IV. FIG. 2C is analignment of LysM domains from the LYK Group II, which contains LysMmotif Types I, II and V. FIG. 2D is an alignment of LysM domains fromthe LYK Group III, which contains LysM motif Type VII. FIG. 2E is analignment of LysM domains from the LYP group, which typically containsLysM motif Types VI and VII, or VI and VIII. See also FIG. 1B. FIG. 2Fis an alignment of LysM domains from the LysMe group, which typicallycontains LysM motif Types IX or X. FIG. 2G is an alignment of LysMdomains from the LysMn group, which typically contains LysM motif TypeXI.

As predicted by Pfam, LYP proteins have exactly two LysM motifs andLysMe and LysMn proteins have only one LysM motif. Sequence alignmentsshow that, among the 11 types of LysM motifs, motif sequences of LysMn(the motif within LysMn proteins, LysM motif type XI), one group ofLysMe (the motif within LysMe proteins, LysM motif type X), and onegroup of LYPb (the second motif from the N terminus within LYP proteins,LysM motif VII) are extremely conserved. In these motifs, the amino acididentities averaged across the alignments are 91% for LysMe (type X),86% for LysMn (type XI), and 75% for LYP (type VII). LysMn motifsequences always start with a His and end with a Pro. Similarly, LYPbmotif sequences always end with a Pro. LYKa motifs are seven to 10residues shorter.

In one aspect of this disclosure, soybean plants may be made resistantto soybean rust where no durable resistance is currently available.Certain soybean strains may be susceptible to rust diseases because theylack a functional signaling pathway that can perceive the existence ofchitin or pass such a signal into the plant cell. Other strains may lackcertain functional chitin responsive proteins and thus are not capableof mounting successful defenses against the invaders. It is herebydisclosed a methodology whereby a transgene encoding a component of thechitin signaling pathway may be introduced into a plant, such as asoybean plant. Expression of the transgene may enhance the perception ofchitin by the transgenic plant, augment subsequent signaling that leadsto gene activation inside the cells, and/or increase the capability ofeffector proteins in fighting the fungal pathogens.

In another aspect, mutations may be identified, induced or introducedinto a plant, such as soybean, in order to obtain a mutant plant thathave enhanced chitin perception or response. Certain mutations in LysMRLKs may enhance recognition of chitin by plant cells, whereas someother mutations in LysM RLKs may abolish chitin recognition. Similarsituations may apply to other protein involved in fungal defense,including but not limited to the CRGs. The polynucleotide sequencesdisclosed herein may aid identification, mapping and/or genetic analysisof such mutants.

In one embodiment, a transgenic plant may be prepared by identifying ina plant one or more genes that contain a LysM receptor kinase familygene with a level of expression that is regulated by treatment of theplant with chitin. Such a plant may then be transformed with one or moreLysM receptor kinase genes. The resulting transgenic plant may bechallenged with chitin, its derivatives, or a pathogen to confirm anenhanced plant defense response, if desired.

The same general techniques disclosed herein may be employed in plantsother than soybean to help create strains that are resistant to fungalinfection. Different plants may be used to effect the transformation,such as soybean, Arabidopsis thaliana, or others. For instance, genesidentified in one species may be introduced into another species inorder to obtain transgenic plants that have enhanced fungal defense.

In another embodiment, a gene which belongs to the LysM receptor kinasefamily may be knocked out. Alternatively, a LysM receptor kinase familygene may be overexpressed. The resultant mutant plants may exhibitimproved plant defense responses when challenged with chitin or itsderivatives, for example, by spraying the leaves with chitin, or whenchallenged with a chitin-expressing organism.

In another embodiment, the LysM receptor kinase family gene may be anygenes having a coding sequence that has 70%, 80%, 90%, 95%, 99%, or 100%sequence identity to any one of the polynucleotides of SEQ ID Nos. 1-7and 54-95. In another embodiment, the LysM receptor kinase family genemay be any genes having a coding sequence that has 70%, 80%, 90%, 95%,99%, or 100% sequence identity to the polynucleotides of SEQ ID No. 6(AtLyk4).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates the eleven distinct types of LysM motifs in plants.FIG. 1(A) The evolutionary relationships of plant LysM motifs. FIG. 1(B)Subcellular localization and LysM domain structures of LysM proteins inplants.

FIGS. 2A-2G show a sequence comparison of various plant LysM sequencesthat were obtained by computerized searching. FIG. 2A shows an alignmentof 93 LysM-containing proteins: MtLYK10 (SEQ ID No. 75), MtLYK11 (SEQ IDNo. 76), MtLysMe2 (SEQ ID No. 150; HtLYK1 (SEQ ID No. 71); MtLysHe1 (SEQID No. 151); AtLYK1 (SEQ ID No. 3); GmLYK2 (SEQ ID No. J6); HtLYK3 (SEQID No. 72); HtLYK4 (SEQ ID No. 73); HtLYK2 (SEQ ID No. 152); LjNFR1a(SEQ ID No. 1); PtLysHn8 (SEQ ID No. 153); PtLYK1 (SEQ ID No. 85);GmLYK8 (SEQ ID No. 63); PtLYK3 (SEQ ID No. 87); AtLYK5 (SEQ ID No. 5);GmLYK6 (SEQ ID No. 61); GmLYK4 (SEQ ID No. 58); HtLYK12 (SEQ ID No. 77);PtLYK6 (SEQ ID No. 90); PtLYK9 (SEQ ID No. 93); AtLYK4 (SEQ ID No. 6);OsLYK1 (SEQ ID No. 79); PtLYK5 (SEQ ID No. 89); GnLYK10 (SEQ ID No. 65);PtLYK7 (SEQ ID No. 91); AtLYK2 (SEQ ID No. 4); OsLYK2 (SEQ ID No. 80);PtLYP1 (SEQ ID No. 154); PtLYK4 (SEQ ID No. 88); PtLYK10 (SEQ ID No.94); GmLYK9 (SEQ ID No. 64); GnNFR5a (SEQ ID No. 59); LjNFR5 (SEQ ID No.2); PsSYH10 (SEQ ID No. 155); HtLYK13 (SEQ ID No. 78); HtLYK9 (SEQ IDNo. 74); PtLYK2 (SEQ ID No. 86); OsLYK3 (SEQ ID No. 81); AtLYK3 (SEQ IDNo. 5); PtLYK8 (SEQ ID No. 92); GnLYK11 (SEQ ID No. 66); PtLYP2 (SEQ IDNo. 156); PtLYP3 (SEQ ID No. 157); PtLYP6 (SEQ ID No. 158); AtLYP3 (SEQID No. 159); GmLYP1 (SEQ ID No. 160); OsLYP1 (SEQ ID No. 161); PtLYP7(SEQ ID No. 162); PtLYP5 (SEQ ID No. 163); PtLYP4 (SEQ ID No. 164);GmLYP4 (SEQ ID No. 165); GmLYP2 (SEQ ID No. 166); AtLYP2 (SEQ ID No.167); AtLYP2 (SEQ ID No. 168); GmLYP3 (SEQ ID No. 169); GmLysHe1 (SEQ IDNo. 170); MtLysH16 (171); PtLysHe7 (SEQ ID No. 172); GmLysHe2 (SEQ IDNo. 173); GmLysHe4 (SEQ ID No. 174); PtLysHe6 (SEQ ID No. 175); GmLysHe3(SEQ ID No. 176); GmLysHe6 (SEQ ID No. 177); GmLysHe5 (SEQ ID No. 178);PtLysHe3 (SEQ ID No. 179); PtLysHe5 (SEQ ID No. 180); PtLysMe10 (SEQ IDNo. 181); AtLysHe3 (SEQ ID No. 182); OsLysHe4 (SEQ ID No. 183); AtLysHe2(SEQ ID No. 184); AtLysHe1 (SEQ ID No. 185); PtLysHn9 (SEQ ID No. 186);PtLysHn7 (SEQ ID No. 187); PtLysHe8 (SEQ ID No. 188); PtLysMe11 (SEQ IDNo. 189); PtLysHe4 (SEQ ID No. 190); GmLysHn2 (SEQ ID No. 191); GmLysHn4(SEQ ID No. 192); PtLysHn6 (SEQ ID No. 193); OsLysHn3 (SEQ ID No. 194);GmLysHn3 (SEQ ID No. 195); GmLysHn5 (SEQ ID No. 196); AtLysHn2 (SEQ IDNo. 197); PtLysMn11 (SEQ ID No. 198); AtLysHn3 (SEQ ID No. 199);GmLysHn1 (SEQ ID No. 200); AtLysHn1 (SEQ ID No. 201); PtLysHn2 (SEQ IDNo. 202); PtLysHn1 (SEQ ID No. 203); OsLysHn1 (SEQ ID No. 204);PtLysMn10 (SEQ ID No. 205); and PtLysHe9 (SEQ ID No. 206). FIG. 2B is analignment of LysM domains from the following proteins: MtLYK3 (SEQ IDNo. 72), MtLYK4 (SEQ ID No. 73), MtLYK2 (SEQ ID No. 152), GmNFR1a (SEQID No. 54; GmNFR1b (SEQ ID No. 55); LjNFR1a (SEQ ID No. 1); MtLYK1 (SEQID No. 71); AtLYK1 (SEQ ID No. 3); GmLYK3 (SEQ ID No. 57); MtLYK3 (SEQID No. 72); MtLYK4 (SEQ ID No. 73); MtLYK2 (SEQ ID No. 152); GmNFR1a(SEQ ID No. 54); GmNFR1b (SEQ ID No. 55); LjNFR1a (SEQ ID No. 1); MtLYK1(SEQ ID No. 71); AtLYK1 (SEQ ID No. 3); and GmLYK3 (SEQ ID No. 57). FIG.2C is an alignment of LysM domains from GmNFR5a (SEQ ID No. 59); LjNFR5(SEQ ID No. 2); MtLYK9 (SEQ ID No. 74); PtLYK2 (SEQ ID No. 86); GmLYK10(SEQ ID No. 65); PtLYK7 (SEQ ID No. 91); AtLYK5 (SEQ ID No. 7); GmLYK8(SEQ ID No. 63); MtLYK10 (SEQ ID No. 75); MtLYK11 (SEQ ID No. 76);LjLYK4 (SEQ ID No. 69); MtLYK12 (SEQ ID No. 77); GmLYK4 (SEQ ID No. 58);PtLYK6 (SEQ ID No. 90); PtLYK9 (SEQ ID No. 93); AtLYK4 (SEQ ID No. 6);PtLYK10 (SEQ ID No. 94); PtLYK4 (SEQ ID No. 88); GmLYK9 (SEQ ID No. 62);MtLYK13 (SEQ ID No. 78); PsSYM10 (SEQ ID No. 155); PtLYK11 (SEQ ID No.95); GmNFR5b (SEQ ID No. 60); GmNFR5a (SEQ ID No. 59); LjNFR5 (SEQ IDNo. 2); MtLYK9 (SEQ ID No. 74); PtLYK2 (SEQ ID No. 86); GmLYK10 (SEQ IDNo. 65); PtLYK7 (SEQ ID No. 91); AtLYK5 (SEQ ID No. 7); GmLYK8 (SEQ IDNo. 63); MtLYK10 (SEQ ID No. 75); MtLYK11 (SEQ ID No. 76); LyLYK4 (SEQID No. 69); MtLYK12 (SEQ ID No. 77); GmLYK4 (SEQ ID No. 58); PtLYK6 (SEQID No. 90); PtLYK9 (SEQ ID No. 93); AtLYK4 (SEQ ID No. 6); PtLYK10 (SEQID No. 94); PtLYK4 (SEQ ID No. 88); GmLYK9 (SEQ ID No. 64); MtLYK13 (SEQID No. 78); PsSYM10 (SEQ ID No. 155); PtLYK11 (SEQ ID No. 95); andGmNFR5b (SEQ ID No. 60). FIG. 2D is an alignment of LysM domains fromGmLYK6 (SEQ ID No. 61); PtLYK3 (SEQ ID No. 87); OsLYK1 (SEQ ID No. 79);PtLYK5 (SEQ ID No. 89); AtLYK2 (SEQ ID No. 4); GmLKY11 (SEQ ID No. 66);PtLYK8 (SEQ ID No. 92); AtLYK3 (SEQ ID No. 5); OsLYK2 (SEQ ID No. 80);PtLYK1 (SEQ ID No. 85); OsLYK3 (SEQ ID No. 81). FIG. 2E is an alignmentof LysM domains from AtLyP1 (SEQ ID No. 167); AtLYP2 (SEQ ID No. 168);PtLYP5 (SEQ ID No. 163); PtLYP7 (SEQ ID No. 162); PtLYP4 (SEQ ID No.164); GmLYP4 (SEQ ID No. 165); GmLYP2 (SEQ ID No. 166); OsLYP3 (SEQ IDNo. 207); OsLYP5 (SEQ ID No. 208); OsLYP4 (SEQ ID No. 209); GmLYP3 (SEQID No. 169); OsLYP1 (SEQ ID No. 161); OsLYP6 (SEQ ID No. 210); OsLYP2(SEQ ID No. 211); PtLYP2 (SEQ ID No. 156); PtLYP3 (SEQ ID No. 157);AtLYP3 (SEQ ID No. 159); GmLYP1 (SEQ ID No. 160; PtLYP6 (SEQ ID No.158); and PtLYP1 (SEQ ID No. 154). FIG. 2F is an alignment of LysMdomains from GMLYSMe1 (SEQ ID No. 170); PtLysMe7 (SEQ ID No. 172);AtLysMe1 (SEQ ID No. 185); AtLysMe3 (SEQ ID No. 182); GmLysMe4 (SEQ IDNo. 174); GmLysMe2 (SEQ ID No. 173); GmLysMe3 (SEQ ID No. 176); GmLysMe5(SEQ ID No. 178); GmLysMe6 (SEQ ID No. 177); PtLysMe6 (SEQ ID No. 175);PtLysMe3 (SEQ ID No. 179); PtLysMe5 (SEQ ID No. 180); PtLysMe10 (SEQ IDNo. 181); OsLysMe4 (SEQ ID No. 183); AtLysMe2 (SEQ ID No. 184);PtLysMe11 (SEQ ID No. 189); PtLysMe8 (SEQ ID No. 188); PtLysMe4 (SEQ IDNo. 190); OsLysMe2 (SEQ ID No. 212); OsLysMe1 (SEQ ID No. 213); PtLysMe9(SEQ ID No. 206); OsLysMe3 (SEQ ID No. 214). FIG. 2G is an alignment ofLysM domains from AtLYSMn1 (SEQ ID No. 201); AtLysMn1 (SEQ ID No. 201);GmLysMn1 (SEQ ID No. 200); PtLysMn2 (SEQ ID No. 202); PtLysMn1 (SEQ IDNo. 203); OsLysMn1 (SEQ ID No. 204); GmLysMn2 (SEQ ID No. 191); GmLysMn4(SEQ ID No. 192); PtLysMn6 (SEQ ID No. 193); OsLysMn3 (SEQ ID No. 194);GmLysMn3 (SEQ ID No. 195); GmLysMn5 (SEQ ID No. 196); AtLysMn2 (SEQ IDNo. 197); PtLysMn11 (SEQ ID No. 198); AtLysMn3 (SEQ ID No. 199);OsLysMn2 (SEQ ID No. 215); PtLysMn10 (SEQ ID No. 205); PtLysMn7 (SEQ IDNo. 187); PtLysMn9 (SEQ ID No. 186); and PtLysMn8 (SEQ ID No. 153).

FIG. 3 presents experimental results showing enhanced expression of thedefense genes PR-1 and PR-2 in the LysM receptor kinase mutant L3. FIG.3A shows enhanced expression of the defense gene PR-2 in the LysMreceptor kinase mutant L3. FIG. 3B shows enhanced expression of thedefense gene PR-1 in the LysM receptor kinase mutant L3.

FIG. 4A shows an improved defense response of the L3 mutant to infectionby the necotrophic fungus Botrytis cinerea.

FIG. 4B shows an improved defense response of the L3 mutant to infectionby Pseudomonas syringae.

FIG. 5 shows a model of the involvement of the LysM receptor kinases inplant defense.

FIG. 6 shows that the knockout of the AtLysM RLK1 gene blocks theinduction of the selected chitooligosaccharide-responsive genes (CRGs).FIG. 6A shows that induction of all selected CRGs is almost completelyblocked in another insertion mutant, corresponding to At3g21630, orAtLYK1 (designated hereafter as AtLysM RLK1). FIG. 6B illustrates theintron-exon structure of AtLysM RLK1 (Square boxes represent exons.Solid lines between them are introns). FIG. 6C illustrates the predicteddomain structure of AtLysM RLK1 (S: signal peptide; LysM: LysM domain;TM: transmembrane domain; Ser/Thr Kinase: Serine/Threonine kinasedomain)

FIG. 7 shows disruption of the AtLysM RLK1 gene expression by the T-DNAinsertions. WT=Wild-type Col-0; Mu=AtLysM RLK1 mutant. Actin-2 was usedas an internal control. FIG. 7A shows RT-PCR results showing thatprimers corresponding to the exon regions on the side of the 10th intronfailed to detect mRNA expression in the AtLysM RLK1 mutant. FIG. 7Bshows that a truncated transcript derived from the gene sequence beforethe intron can be detected in the mutant by RT-PCR.

FIG. 8 shows restoration of CRGs in the AtLysM RLK1 mutant by theectopic expression of the AtLysM RLK1 gene. Actin-2 serves as aninternal control.

FIG. 9 shows the tissue expression pattern of the AtLysM RLK1 gene.Actin-2 serves as an internal control.

FIG. 10 shows that AtLysM RLK1 is induced by chitooligosaccharides, butnot by the flagellin-derived flg22 peptide.

FIG. 11 shows that the T-DNA insertions in the AtLysM RLK1 gene blockthe induction of virtually all CRGs. FIG. 11A is a microarray read-outshowing that a total of 909 genes responded more than 1.5 fold (P<0.05)to chitooctaose elicitation in both the wild-type and mutant plants 30minutes after the treatment with chitooctaose. FIG. 11B shows the numberof genes that are up-regualted in the wild-type and the mutant out ofthe 909 genes tested. FIG. 11C shows the number of genes that aredown-regualted in the wild-type and the mutant out of the 909 genestested.

FIG. 12 shows the functional categorization by annotations of 909CRGs-GO Biological Process.

FIG. 13 shows that the AtLysM RLK1 mutant is more susceptible to fungalpathogens than wild-type plants and that exogenously appliedchitooligosaccharides enhances resistance in the wild-type plants, butnot in the mutant. FIG. 13A shows photographs of the infected leaves sixdays after inoculation. FIG. 13B shows trypan blue staining of theinfected leaves indicating that the AtLysM RLK1 mutant supported morehyphal growth and production of conidiophores earlier than the wild-typeplants (FIG. 13B). Arrows indicate sites where conidiophores areforming. FIG. 13C shows photographs of the leaves of the plants threedays after inoculation, showing that the mutant developed slightlybigger lesions than the wild-type plants, as measured by averagediameter of the lesions. FIG. 13D shows lesion size of the mutant ascompared to that of wild-type plants. FIG. 13E shows that the mutantplants produced more spores per lesion than the wild-type plants. FIG.13F shows that defense against bacterial infection was not affected bythe mutation.

FIG. 14 shows that the selected CRGs are still induced in the AtLysMRLK1 mutant by a fungal pathogen, but to a reduced level. FIG. 14A showsthat chitin-responsive defense gene MPK3 was induced by the fungalpathogen A. brassicicola in the mutant, albeit to a lower level ascompared to that in wild-type plants. FIG. 14B shows thatchitin-responsive defense gene WRKY53 was induced by the fungal pathogenA. brassicicola in the mutant, albeit to a lower level as compared tothat in wild-type plants.

FIG. 15 shows that mutations in the legume Nod signal receptor genesNFR1 and NFR5 do not affect the induction of the selected CRGs in Lotusjaponicus.

FIG. 16 shows that the mutation in the AtLysM RLK1 gene does not affectother defense-related pathways. FIG. 16A shows that both the mutant andwild-type plants showed similar induction of PR-1 by SA as shown byquantitative RT-PCR. FIG. 16B shows that both the mutant and wild-typeplants showed similar induction of PDF1.2 by MeJA or ACC as shown byquantitative RT-PCR. FIG. 16C shows that the mutant plants were fullyresponsive to another typical PAMP, the flagellin-derived peptide flg22.

FIG. 17 shows that the AtLysM RLK1 mutation does not block the inductionof flagellin-responsive genes.

FIG. 18 shows similarity between the LysM receptor kinase-like genes ina variety of plants.

FIG. 19 shows the expression analysis of GmLysM receptor-like kinases inresponse to white-mold pathogen.

FIG. 20 shows the expression analysis of GmLysM receptor-like kinases inchitin-treated leaves.

FIG. 21 shows the results of tissue-specific expression analysis of LysMreceptor-like kinases in soybean, M. truncatula, and rice.

DETAILED DESCRIPTION

The following detailed description is provided to aid those skilled inthe art in practicing the present instrumentalities. Even so, thisdetailed description should not be construed to unduly limit the presentinvention as modifications and variations in the embodiments discussedherein can be made by those of ordinary skill in the art withoutdeparting from the spirit or scope of the present inventive discovery.

LysM domain-containing receptor-like kinases (“LysM RLKs,” “LYK” or“LysM receptor kinase family proteins”), such as NFR1 and NFR5 inlegumes, have been shown to be critical for the perception of modifiedchitooligosaccharides—Nod signals—in the legume-rhizobial symbioticnodulation process. See Limpens et al., 2003; Madsen et al., 2003; andRadutoiu et al., 2003. Similar LysM receptor kinase family genes (orLysM RLK genes) are also present in non-leguminous plants. Zhang et al.,2007. For example, five LysM RLK genes have been identified in the modelplant Arabidopsis thaliana. LysM domain-containing proteins are alsofound in animals but LysM RLKs appear to be unique to plants. Zhang etal., 2007.

For purpose of this disclosure, a “LysM receptor kinase family gene”(LysM RLK gene) is any gene that encodes a protein with at least aLysine motif (LysM) domain, a kinase domain and a transmembrane domainbetween the LysM and the kinase domain as shown in FIG. 1. In oneaspect, the kinase domain is a serine/threonine kinase domain. A genemay be shown to belong to different subfamilies of LysM genes bysequence comparison with a known LysM gene, as exemplified by thesequence alignment of different LysM containing proteins in FIG. 2. Thisclassification may be decided by a predetermined level of sequenceidentity in one or more functional domains of a known LysM receptorkinase, such as 70%, 80%, 90%, 95%, 96%, 97%, 98% 99% or 100% sequenceidentity with respect to a functional domain or an entire codingsequence.

Two sequences may be said to have “substantial sequence similarity” whenthey have a degree of sequence identity that persons of ordinary skillin the art may expect them to provide similar functionality; or in somecases, a person of skills in the art may expect individual domainswithin the sequences to possess similar functionality due to thesequence similarity. As measured by computer algorithms that aredesigned to quantitate sequence identity or similarity, this may be atleast 70% identity, or more preferably, this may be any value from 90%and up, such as 95%, 96%, 97%, 98% or 99% identity, with 100% identitybeing an exact match. When two sequences are of different length, thesequence identity refers to cumulative sequence identity between thosesegments of both sequences that when aligned generate the best possiblematches of individual residues throughout the full length of thesequences. In general, higher sequence similarity between two sequencesindicates that the two sequences are more likely to perform similar, ifnot identical function.

The term CRGs (or CRG) refers to genes that may be activated uponperception of chitin or its derivatives by plant cells. Examples of CRGsmay include MPK3, WRKY22, WRKY29, WRKY33, WRKY53 and any other geneswhose expression levels may be up- or down-regulated when the cells areexposed to chitin or its derivatives. In one embodiment, geneticengineering may be used to render certain CRGs constitutively expressed,or, more preferably, expression of CRGs may be placed under control ofcertain regulatory elements such that CRG proteins may be expressedbefore fungi have been detected by the plant.

Under certain circumstances, it may be desirable to generate mutationsin the coding sequence of certain genes, such as the LYK genes or CRGs.One of skills in the art may recognize that certain sequence variationsmay not significantly affect the functionality of a DNA or RNA molecule,or a protein. For instance, one may align and compare the sequences ofthe LYK family genes, as shown in FIG. 2, to determine which residuesmay be less conservative than others. The term “conservative” is used todepict those nucleotide or amino acid residues that have not undergonesignificant changes over the course of evolution. The conservativeresidues are typically shown as matching residues in a multi-sequencealignment. Guided by such an alignment, one may substitue those residuesthat are less conservative without compromising the functionality of thegenes, RNAs, or proteins. Such manipulations of polynucleotide orpolypeptide molecules are within the scope of this disclosure.

A “functional” LysM receptor kinase refers to a protein encoded by oneof the LysM receptor kinase family genes that is capable of performingthe full function that is typically performed by other LysM receptorkinase family proteins.

“Secretion sequence” means a sequence that directs newly synthesizedsecretory or membrane proteins to and through membranes of theendoplasmic reticulum, or from the cytoplasm to the periplasm across theinner membrane of bacteria, or from the matrix of mitochondria into theinner space, or from the stroma of chloroplasts into the thylakoid.Fusion of such a sequence to a gene that is to be expressed in aheterologous host ensures secretion of the recombinant protein from thehost cell.

A “recombinant polynucleotide” means a polynucleotide that is free ofone or both of the nucleotide sequences which flank the polynucleotidein the naturally-occurring genome of the organism from which thepolynucleotide is derived. The term includes, for example, apolynucleotide or fragment thereof that is incorporated into a vector orexpression cassette; into an autonomously replicating plasmid or virus;into the genomic DNA of a prokaryote or eukaryote; or that exists as aseparate molecule independent of other polynucleotides. It also includesa recombinant polynucleotide that is part of a hybrid polynucleotide,for example, one encoding a polypeptide sequence.

“PCR” means polymerase chain reaction.

As used herein “polynucleotide” and “oligonucleotide” are usedinterchangeably and refer to a polymeric (2 or more monomers) form ofnucleotides of any length, either ribonucleotides ordeoxyribonucleotides. Although nucleotides are usually joined byphosphodiester linkages, the term also includes polymeric nucleotidescontaining neutral amide backbone linkages composed of aminoethylglycine units. This term refers only to the primary structure of themolecule. Thus, this term includes double- and single-stranded DNA andRNA. It also includes known types of modifications, for example, labels,methylation, “caps”, substitution of one or more of the naturallyoccurring nucleotides with an analog, internucleotide modifications suchas, for example, those with uncharged linkages (e.g., methylphosphonates, phosphotriesters, phosphoamidates, carbamates, etc.),those containing pendant moieties, such as, for example, proteins(including for e.g., nucleases, toxins, antibodies, signal peptides,poly-L-lysine, etc.), those with intercalators (e.g., acridine,psoralen, etc.), those containing chelators (e.g., metals, radioactivemetals, boron, oxidative metals, etc.), those containing alkylators,those with modified linkages (e.g., alpha anomeric nucleic acids, etc.),as well as unmodified forms of the polynucleotide. Polynucleotidesinclude both sense and antisense strands.

“Sequence” means the linear order in which monomers occur in a polymer,for example, the order of amino acids in a polypeptide or the order ofnucleotides in a polynucleotide.

“Peptide,” “Protein” and “Polypeptide” are used interchangeably and meana compound that consists of two or more amino acids that are linked bymeans of peptide bonds.

“Recombinant protein” means that the protein, whether comprising anative or mutant primary amino acid sequence, is obtained by expressionof a gene carried by a recombinant DNA molecule in a cell other than thecell in which that gene and/or protein is naturally found. In otherwords, the gene is heterologous to the host in which it is expressed. Itshould be noted that any alteration of a gene, including the addition ofa polynucleotide encoding an affinity purification moiety, makes thatgene unnatural for the purposes of this definition, and thus that genecannot be “naturally” found in any cell.

A “non-immunoglobulin peptide” means a peptide which is not animmunoglobulin, a recognized region of an immunoglobulin, or contains aregion of an immunoglobulin. For example, a single chain variable regionof an immunoglobulin would be excluded from this definition.

“Substantially pure” or “substantially purified” means that thesubstance is free from other contaminating proteins, nucleic acids, andother biologicals derived from the original source organism. Purity maybe assayed by standard methods, and will ordinarily be at least about40% pure, more ordinarily at least about 50% pure, generally at leastabout 60% pure, more generally at least about 70% pure, often at leastabout 75% pure, more often at least about 80% pure, typically at leastabout 85% pure, more typically at least about 90% pure, preferably atleast about 95% pure, more preferably at least about 98% pure, and ineven more preferred embodiments, at least 99% pure. The analysis may beweight or molar percentages, evaluated, e.g., by gel staining,spectrophotometry, or terminus labeling etc.

A “transgene” refers to a coding sequence that has been introduced intoa host organism, which may be referred to as a transgenic organism,e.g., a transgenic animal, or a transgenic plant, when the transgene hasbeen successfully introduced into said organism. Typically, a transgeneis introduced into a host organism so that the coding sequence may betranscribed into RNA or, in most cases, be further expressed as apolypeptide. The introduction of a transgene into a host organism andsubsequent expression of the transgene is generally known as atransgenic process. A transgenic plant may refer to a whole plant, or atissue of a plant, such as a seed, that contains a transgene and has apotential to be grow into a plant.

A “mutation,” as used herein, means a change in the nucleotide sequenceof a polynucleotide molecule or a change in the amino acid sequence of apolypeptide. The molecule carrying such a change may be referred to as amutant molecule, and the change is typically measured by comparing thesequence of the mutant molecule with that of the polynucleotide orpolypeptide molecule from which the mutant molecule is derived. Anorganism with a mutation in one of its endogenous genes may be called amutant.

A mutation in a gene may occur on either the coding region or thenon-coding region of the gene. A mutated copy of a gene may be said tobe “derived” from a endogenous copy of the same gene when one or morespontaneous or induced mutations occur on an endogenous gene, at whichpoint the endogenous gene becomes a mutated gene because it is no longerthe same as the original wild-type gene. The resultant organism may becalled a mutant.

In one aspect, the polynucleotide sequences disclosed herein, includingbut not limited to LysM receptor kinase family genes and various CRGs,may be used to identify those mutants with mutations in one of the LysMreceptor kinase family genes. For instance, a large number of mutantsmay be generated by either spontaneous or induced mutation. Thesemutants may be screened to identify those mutations that occur in one ofthe LysM receptor kinase family genes. Suitable methods for such ascreening may include, for example, PCR, sequencing, or hybridization.

In another aspect, these polynucleotide sequences, including but notlimited to LysM receptor kinase family genes and various CRGs, may alsobe used to design DNA construct for targeted insertion, deletion, orsubstitution of a specific LysM receptor kinase family gene. Forinstance, a DNA fragment may be first inserted into the coding region ofa LysM receptor kinase family gene, the construct thus obtained may thenbe introduced into a host to create an insertional mutant by homologousrecombination.

The traits of a plant may be modified. A modified plant may becoconsidered “fungal resistant” if the chance of a plant becominginfected by a specific fungal pathogen is at least 30% less than that ofa wild-type plant from which the modified plant is derived.

A molecule is “endogenous” to an organism if the molecule exists or isencoded by a molecule that exists in the organism without requiring atransgenic process. For purpose of this disclosure, the terms“expression” and “express” refer to transcription of DNA into RNA, ortranslation of RNA into protein, or both.

Besides null mutation that renders a protein completely non-functional,a mutation may also render a protein dominant negative when it onlyabolishes partial function of a protein. The resultant partiallyfunctioning protein may act as a “dominant negative” protein when itcontinues to perform the remaining function. For example, a mutatedprotein may continue to bind a co-factor without activating thatco-factor because the activation function has been lost. When such amutated protein is expressed in a cell, it binds to many co-factorswithout activating them, thus rendering them unavailable for thewild-type protein. In this situation, the mutant protein is said to beacting in a dominant negative fashion.

The term “knocking out” or “knock out” means rendering a genenon-functional. “Knocking down” means lowering the expression levels ofa gene or decrease the relative activity of the encoded protein. A genecan be knocked out or knocked down through deletion, insertion,substitution of a fragment or a residue in the coding region or in theregulatory regions of a gene.

Within the scope of the disclosed instrumentalities are recombinantoligonucleotides encoding peptides having antifungal activity. Theserecombinant oligonucleotides can be used to produce recombinantpolynucleotides which are commonly used as cloning or expression vectorsalthough other uses are possible. A cloning vector is a self-replicatingDNA molecule that serves to transfer a DNA segment into a host cell. Thethree most common types of cloning vectors are bacterial plasmids,phages, and other viruses. An expression vector is a cloning vectordesigned so that a coding sequence inserted at a particular site will betranscribed and translated into a protein.

Both cloning and expression vectors may contain nucleotide sequencesthat allow the vectors to replicate in one or more suitable host cells.In cloning vectors, this sequence is generally one that enables thevector to replicate independently of the host cell chromosomes, and alsoincludes either origins of replication or autonomously replicatingsequences. Various bacterial and viral origins of replication are wellknown to those skilled in the art and include, but are not limited tothe pBR322 plasmid origin, the 2μ plasmid origin, and the SV40, polyoma,adenovirus, VSV and BPV viral origins. An expression vector may containan origin of replication so that it can be replicated independently fromthe host's chromosome. More preferably, an expression vector carryingthe transgene of interest may have a means by which the DNA fragmentcontaining the transgene may be integrated onto a chromosome of the hostplant and thus may be replicated along with the host chromosomes.

The polynucleotide sequences of the present disclosure may be used toproduce antifungal peptides by the use of recombinant expression vectorscontaining the polynucleotide sequence disclosed herein. For purpose ofthis disclosure, antifungal peptides may mean polypeptides or fragmentsthereof that may help prevent fungal infection of a plant. Examples ofantifungal peptides may include but not limited to polypeptides encodedby the LysM receptor kinase genes or the CRGs. In one embodiment, theseantifungal peptide may be expressed in vitro and be applied onto a plantor be injected into a plant to achieve the desired antifungal effects.Suitable expression vectors include chromosomal, non-chromosomal andsynthetic DNA sequences, for example, SV 40 derivatives; bacterialplasmids; phage DNA; baculovirus; yeast plasmids; vectors derived fromcombinations of plasmids and phage DNA; and viral DNA such as vaccinia,adenovirus, fowl pox virus, and pseudorabies. In addition, any othervector that is replicable and viable in the host may be used. Suitablehost for in vitro expression may include bacterial, yeast, plant orinsect cells, among others.

The nucleotide sequence of interest may be inserted into the vector by avariety of methods. In the most common method the sequence is insertedinto an appropriate restriction endonuclease site(s) using procedurescommonly known to those skilled in the art and detailed in, for example,Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed., ColdSpring Harbor Press, (1989) and Ausubel et al., Short Protocols inMolecular Biology, 2nd ed., John Wiley & Sons (1992).

In an expression vector, the sequence of interest may be operably linkedto a suitable regulatory elements, including but not limited to apromoter or a enhancer, that may be recognized by the host cell todirect mRNA synthesis. Promoters generally refer to untranslatedsequences located upstream from the start codon of a structural genethat regulate the transcription and translation of nucleic acidsequences under their control. Promoters may be classified as eitherinducible or constitutive promoters. Inducible promoters are promotersthat initiate increased levels of transcription from DNA under theircontrol in response to some change in the environment, e.g. the presenceor absence of a nutrient or a change in temperature. Constitutivepromoters, in contrast, maintain a relatively constant level oftranscription.

A nucleic acid sequence is operably linked when it is placed into afunctional relationship with another nucleic acid sequence. For example,DNA for a presequence or secretory leader is operatively linked to DNAfor a polypeptide if it is expressed as a preprotein which participatesin the secretion of the polypeptide; a promoter is operably linked to acoding sequence if it affects the transcription of the sequence; or aribosome binding site is operably linked to a coding sequence if it ispositioned so as to facilitate translation. Generally, operably linkedsequences are contiguous and, in the case of a secretory leader,contiguous and in reading phase. Linking is achieved by ligation atrestriction enzyme sites. If suitable restriction sites are notavailable, then synthetic oligonucleotide adapters or linkers can beused as is known to those skilled in the art. Sambrook et al., MolecularCloning, A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, (1989)and Ausubel et al., Short Protocols in Molecular Biology, 2nd ed., JohnWiley & Sons (1992).

Common promoters used in expression vectors include, but are not limitedto, LTR or SV40 promoter, the E. coli lac or trp promoters, and thephage lambda PL promoter. Useful inducible plant promoters includeheat-shock promoters (Ou-Lee et al. (1986) Proc. Natl. Acad. Sci. USA83: 6815; Ainley et al. (1990) Plant Mol. Biol. 14: 949), anitrate-inducible promoter derived from the spinach nitrite reductasegene (Back et al. (1991) Plant Mol. Biol. 17: 9), hormone-induciblepromoters (Yamaguchi-Shinozaki et al. (1990) Plant Mol. Biol. 15: 905;Kares et al. (1990) Plant Mol. Biol. 15: 905), and light-induciblepromoters associated with the small subunit of RuBP carboxylase and LHCPgene families (Kuhlemeier et al. (1989) Plant Cell 1: 471; Feinbaum etal. (1991) Mol. Gen. Genet. 226: 449; Weisshaar et al. (1991) EMBO J.10: 1777; Lam and Chua (1990) Science 248: 471; Castresana et al. (1988)EMBO J. 7: 1929; Schulze-Lefert et al. (1989) EMBO J. 8: 651). Otherpromoters known to control the expression of genes in prokaryotic oreukaryotic cells can be used and are known to those skilled in the art.Expression vectors may also contain a ribosome binding site fortranslation initiation, and a transcription terminator. The vector mayalso contain sequences useful for the amplification of gene expression.

Expression and cloning vectors can, and usually do, contain a selectiongene or selection marker. Typically, this gene encodes a proteinnecessary for the survival or growth of the host cell transformed withthe vector. Examples of suitable markers include dihydrofolate reductase(DHFR) or neomycin resistance for eukaryotic cells and tetracycline orampicillin resistance for E. coli. Selection markers in plants includeresistance to bleomycin, gentamycin, glyphosate, hygromycin, kanamycin,methotrexate, phleomycin, phosphinotricin, spectinomycin, streptomycin,sulfonamide and sulfonylureas. Maliga et al., Methods in Plant MolecularBiology, Cold Spring Harbor Press, 1995, p. 39.

In addition, expression vectors can also contain marker sequencesoperatively linked to a nucleotide sequence for a protein that encode anadditional protein used as a marker. The result is a hybrid or fusionprotein comprising two linked and different proteins. The marker proteincan provide, for example, an immunological or enzymatic marker for therecombinant protein produced by the expression vector. Suitable markersinclude, but are not limited to, alkaline phosphatase (AP), myc,hemagglutinin (HA), β-glucuronidase (GUS), luciferase, and greenfluorescent protein (GFP).

The polynucleotide sequences of the present disclosure may also be partof an expression cassette that at a minimum comprises, operably linkedin the 5′ to 3′ direction, a regulatory sequence such as a promoter, apolynucleotide encoding a peptide of the present disclosure, and atranscriptional termination signal sequence functional in a host cell.The promoter can be of any of the types discussed herein, for example, atissue specific promoter, a developmentally regulated promoter, anorganelle specific promoter, a seed specific promoter, a plastidspecific promoter, etc. The expression cassette can further comprise anoperably linked targeting, transit, or secretion peptide coding regioncapable of directing transport of the protein produced. The expressioncassette can also further comprise a nucleotide sequence encoding aselectable marker and/or a purification moiety.

More particularly, the present disclosure includes recombinantconstructs comprising an isolated polynucleotide sequence encoding theantifungal peptides of the present disclosure. The constructs caninclude a vector, such as a plasmid or viral vector, into which thesequence has been inserted, either in the forward or reverseorientation. The recombinant construct can further comprise regulatorysequences, including, for example, a promoter operatively linked to thesequence. Large numbers of suitable vectors and promoters are known tothose skilled in the art and are commercially available.

Different domains from different LysM RLKs may be combined to obtainchimeric proteins. Such a chimeric protein may possess a number ofdesirable properties that are not otherwise exhibited by one singleprotein that naturally exist in plants. Such desirable properties mayinclude but are not limited to increased sensibility to chitin and itsderivatives, increased kinase activity or enhanced kinase specificity.

A further embodiment of the present disclosure relates to transformedhost cells containing constructs comprising the oligonucleotidesequences of the present disclosure. For instance, various combinationof the LysM RLK genes, in wild-type or mutated forms, may be introducedas transgenes into a host plant, such as soybean. In a preferredembodiment, the host plants is susceptible to fungal infection and theexpression of the LysM RLK transgenes may confer certain degree offungal resistance to the host. In addition to the LysM RLK genes, thetransgenes may include other genes that may play a role in fungaldefense, such as any of the CRGs whose forced expression may enhance thehost's capability to defend against fungal pathogens.

The host cell can be a higher eukaryotic cell, such as a mammalian orplant cell, or a lower eukaryotic cell such as a yeast cell, or the hostcan be a prokaryotic cell such as a bacterial cell. Introduction of theconstruct into the host cell can be accomplished by a variety of methodsincluding calcium phosphate transfection, DEAE-dextran mediatedtransfection, Polybrene, protoplast fusion, liposomes, directmicroinjection into the nuclei, scrape loading, and electroporation. Inplants, a variety of different methods can be employed to introducetransformation/expression vectors into plant protoplasts, cells, callustissue, leaf discs, meristems, etc., to generate transgenic plants.These methods include, for example, Agrobacterium-mediatedtransformation, particle gun delivery, microinjection, electroporation,polyethylene glycol-mediated protoplast transformation,liposome-mediated transformation, etc. (reviewed in Potrykus (1991)Annu. Rev. Plant Physiol. Plant Mol. Biol. 42: 205).

Peptides produced by expression of the polynucleotides of the presentdisclosure can be obtained by transforming a host cell by any of thepreviously described methods, growing the host cell under appropriateconditions, inducing expression of the polynucleotide and isolating theprotein(s) of interest. If the protein in retained within the host cell,the protein can be obtained by lysis of the host cells, while if theprotein is a secreted protein, it can be isolated from the culturemedium. Several methods are available for purification of proteins andare known to those of ordinary skill in the art. These includeprecipitation by, for example, ammonium sulfate or ethanolprecipitation, acid extraction, anion or cation exchange chromatography,phosphocellulose chromatography, hydrophobic interaction chromatography,affinity chromatography, hydroxylapatite chromatography, lectinchromatography, high performance liquid chromatography (HPLC),electrophoresis under native or denaturing conditions, isoelectricfocusing, and immunoprecipitation.

Alternatively, peptides encoded by the polynucleotides of the presentdisclosure can be produced by chemical synthesis using eithersolid-phase peptide synthesis or by classical solution peptide synthesisalso known as liquid-phase peptide synthesis. In oligomer-supportedliquid phase synthesis, the growing product is attached to a largesoluble polymeric group. The product from each step of the synthesis canthen be separated from unreacted reactants based on the large differencein size between the relatively large polymer-attached product and theunreacted reactants. This permits reactions to take place in homogeneoussolutions, and eliminates tedious purification steps associated withtraditional liquid phase synthesis. Oligomer-supported liquid phasesynthesis has also been adapted to automatic liquid phase synthesis ofpeptides.

For solid-phase peptide synthesis, the procedure entails the sequentialassembly of the appropriate amino acids into a peptide of a desiredsequence while the end of the growing peptide is linked to an insolublesupport. Usually, the carboxyl terminus of the peptide is linked to apolymer from which it can be liberated upon treatment with a cleavagereagent. In a common method, an amino acid is bound to a resin particle,and the peptide generated in a stepwise manner by successive additionsof protected amino acids to produce a chain of amino acids.Modifications of the technique described by Merrifield are commonly used(see, e.g., Merrifield, J. Am. Chem. Soc. 96: 2989-93, 1964). In anautomated solid-phase method, peptides are synthesized by loading thecarboxy-terminal amino acid onto an organic linker (e.g., PAM,4-oxymethylphenylacetamidomethyl), which is covalently attached to aninsoluble polystyrene resin cross-linked with divinyl benzene. Theterminal amine may be protected by blocking with t-butyloxycarbonyl.Hydroxyl- and carboxyl-groups are commonly protected by blocking withO-benzyl groups. Synthesis is accomplished in an automated peptidesynthesizer, a number of which are commercially available. Followingsynthesis, the product may be removed from the resin. The blockinggroups are removed typically by using hydrofluoric acid ortrifluoromethyl sulfonic acid according to established methods (e.g.,Bergot and McCurdy, Applied Biosystems Bulletin, 1987). Followingcleavage and purification, a yield of approximately 60 to 70% istypically produced. Purification of the product peptides is accomplishedby, for example, crystallizing the peptide from an organic solvent suchas methyl-butyl ether, then dissolving in distilled water, and usingdialysis (if the molecular weight of the subject peptide is greater thanabout 500 daltons) or reverse high-pressure liquid chromatography (e.g.,using a C18 column with 0.1% trifluoroacetic acid and acetonitrile assolvents) if the molecular weight of the peptide is less than 500daltons. Purified peptide may be lyophilized and stored in a dry stateuntil use. Analysis of the resulting peptides may be accomplished usingthe common methods of analytical high pressure liquid chromatography(HPLC) and electrospray mass spectrometry (ES-MS).

In general, transgenic plants comprising cells containingpolynucleotides of the present disclosure can be produced by any of theforegoing methods; selecting plant cells that have been transformed on aselective medium; regenerating plant cells that have been transformed toproduce differentiated plants; and selecting a transformed plant thatexpresses the protein(s) encoded by the polynucleotides of the presentdisclosure at a desired level.

Specific methods for transforming a wide variety of dicots and obtainingtransgenic plants are well documented in the literature (Gasser andFraley, Science 244:1293, 1989; Fisk and Dandekar, ScientiaHorticulturae 55:5, 1993; Dandekar and Fisk, Plant transformation:agrobacterium-mediated gene transfer. Methods Mol. Biol. 2005;286:35-46; Olhoft P M, Donovan C M, Somers D A, Soybean (Glycine max)transformation using mature cotyledonary node explants, Methods Mol.Biol. 2006; 343:385-96; Ko T S, Korban S S, Somers D A, Soybean (Glycinemax) transformation using immature cotyledon explants, Methods Mol Biol.2006; 343:397-405; and all references cited therein).

Successful transformation and plant regeneration have also been achievedin a variety of monocots. Specific examples are as follows: asparagus(Asparagus officinalis; Bytebier et al. (1987) Proc. Natl. Acad. Sci.USA 84: 5345); barley (Hordeum vulgarae; Wan and Lemaux (1994) PlantPhysiol. 104: 37); maize (Zea mays; Rhodes et al. (1988) Science 240:204; Gordon-Kamm et al. (1990) Plant Cell 2: 603; Fromm et al. (1990)Bio/Technology 8: 833; Koziel et al. (1993) Bio/Technology 11: 194);oats (Avena sativa; Somers et al. (1992) Bio/Technology 10: 1589);orchardgrass (Dactylis glomerata; Horn et al. (1988) Plant Cell Rep. 7:469); rice (Oryza sativa, including indica and japonica varieties;Toriyama et al. (1988) Bio/Technology 6: 10; Zhang et al. (1988) PlantCell Rep. 7: 379; Luo and Wu (1988) Plant Mol. Biol. Rep. 6: 165; Zhangand Wu (1988) Theor. Appl. Genet. 76: 835; Christou et al. (1991)Bio/Technology 9: 957); rye (Secale cereale; De la Pena et al. (1987)Nature 325: 274); sorghum (Sorghum bicolor; Cassas et al. (1993) Proc.Natl. Acad. Sci. USA 90: 11212); sugar cane (Saccharum spp.; Bower andBirch (1992) Plant J. 2: 409); tall fescue (Festuca arundinacea; Wang etal. (1992) Bio/Technology 10: 691); turfgrass (Agrostis palustris; Zhonget al. (1993) Plant Cell Rep. 13: 1); and wheat (Triticum aestivum;Vasil et al. (1992) Bio/Technology 10: 667; Weeks et al. (1993) PlantPhysiol. 102: 1077; Becker et al. (1994) Plant J. 5: 299). All thesereferences relate to transformation techniques in dicots or monocots andare hereby expressly incorporated into this disclosure by reference.

Various LysM RLK genes show tissue specific expression in plants. Tissuespecific promoters or other regulatory elements may play a role incontrolling these tissue specific expression patterns. DNA recombinationutilizing these regulatory elements may be employed to manipulate theexpression pattern and/or levels of the various LysM RLK genes, or othergenes in general. For instance, expression construct containing a tissuespecific promoter may be used to drive the expression of a LysM RLKwhich is not otherwise expressed in the particular tissue.

EXAMPLES

The following examples are intended to provide illustrations of theapplication of the present disclosure. The following examples are notintended to completely define or otherwise limit the scope of theinvention.

Example 1 Plant LysM Domains are Highly Diversified

The sequences of NFR1 (SEQ ID No. 1) and NFR5 (SEQ ID No. 2) genes fromLotus japonicus, as reported by Radutoiu et al. (2003) were used toidentify genes encoding LysM domain-containing proteins by searchingpublic databases of Arabidopsis, rice, poplar, M. truncatula, and L.japonicus. Soybean LYK genes were identified by shotgun sequencingbacterial artificial chromosomes (BACs) with homologies to LysM-encodingESTs. The resulting putative LYK protein sequences from all species werethen searched against the Pfam server to verify LysM and kinase domains.Collectively, a total of 49 LYK genes were identified in the six plantgenomes, namely, those of Arabidopsis, rice, poplar, M. truncatula, L.japonicus and soybean, as summarized in Table 2. The predicted aminoacid sequences of these genes or fragments were obtained and compared bysequence alignment, with representative alignments shown in FIG. 2.

TABLE 2 LysM type receptor-like kinase genes from Arabidopsis, soybean, Lotus,Medicago, rice and poplar. Name (SEQ ID No.) Alias name SourcesAtLYK1 (SEQ ID No.3) At3g21630 TAIR AtLYK2 (SEQ ID No.4) At3g01840 TAIRAtLYK3 (SEQ ID No.5) At1g51940 TAIR AtLYK4 (SEQ ID No.6) At2g23770 TAIRAtLYK5 (SEQ ID No.7) At2g33580 TAIR GmNFR1α (SEQ ID 54) GmW2098N11.16this study GmNFR1β (SEQ ID 55) GmW2098N15.9 this studyGmLYK2 (SEQ ID 56) GmW2098N11.15 this study GmLYK3 (SEQ ID 57)GmW2026N19.18 this study GmLYK4 (SEQ ID 58) GmW2095P01.22 this studyGmNFR5α (SEQ ID 59) GmW2035N07.17 this study GmNFR5β (SEQ ID 60)GmW2095P01.23 this study GmLYK6 (SEQ ID 61) GmW2075N23 this studyGmLYK7 (SEQ ID 62) GmW2035N07.16 this study GmLYK8 (SEQ ID 63)GmW2098N11.2 this study GmLYK9 (SEQ ID 64) GmW2069O12.22 this studyGmLYK10 (SEQ ID 65) GmW2080D08.12 this study GmLYK11 (SEQ ID 66)GmW2042I24.15 this study LjNFR1 (SEQ ID 1) AJ575248 Gene BankLjLYK2 (SEQ ID 67) TM0545.8 Kazusa LjLYK3 (SEQ ID 68) TM0545.9 KazusaLjLYK4 (SEQ ID 69) TM0522.16 Kazusa LjNFR5 (SEQ ID 2) AJ575255 Gene BankLjLYK6 (SEQ ID 70) TM0076a.10 Kazusa MtLYK1 (SEQ ID 71) CR936945.12Medicago truncatula sequencing resources MtLYK3 (SEQ ID 72) AY372402Gene Bank MtLYK4 (SEQ ID 73) AY372403 Gene Bank MtLYK9 (SEQ ID 74)AC148241_11 Medicago truncatula sequencing resources MtLYK10 (SEQ ID 75)AC148994_13 Medicago truncatula sequencing resources MtLYK11 (SEQ ID 76)AC148994_15 Medicago truncatula sequencing MtLYK12 (SEQ ID 77)AC126779_3 Medicago truncatula sequencing resources MtLYK13 (SEQ ID 78)AC126779_4 Medicago truncatula sequencing resources OsLYK1 (SEQ ID 79)LOC_Os01g36550 TIGR OsLYK2 (SEQ ID 80) LOC_Os06g41980 TIGROsLYK3 (SEQ ID 81) LOC_Os06g41960 TIGR OsLYK4 (SEQ ID 82) LOC_Os02g09960TIGR OsLYK5 (SEQ ID 83) LOC_Os03g13080 TIGR OsLYK6 (SEQ ID 84)LOC_Os11g35330 TIGR PtLYK1 (SEQ ID 85) FGENESH1_PG.C_LG_VIII001701DOE JGI PtLYK2 (SEQ ID 86) FGENESH1_PG.C_LG_VII000997 DOE JGIPtLYK3 (SEQ ID 87) EUGENE3.00051645 DOE JGI PtLYK4 (SEQ ID 88)EUGENE3.00081504 DOE JGI PtLYK5 (SEQ ID 89) EUGENE3.00400189 DOE JGIPtLYK6 (SEQ ID 90) GRAIL3.0019013601 DOE JGI PtLYK7 (SEQ ID 91)GRAIL3.0017002501 DOE JGI PtLYK8 (SEQ ID 92) FGENESH1_PM.C_LG_I000490DOE JGI PtLYK9 (SEQ ID 93) EUGENE3.00570233 DOE JGI PtLYK10 (SEQ ID 94)EUGENE3.00100714 DOE JGI PtLYK11 (SEQ ID 95) eugene3.00570235 DOE JGI

More specifically, plant LysM protein sequences were first searchedusing the key word LysM and BLASTp (1e-20) using the LysM domains ofLjNFR1 (SEQ ID No. 1) and LjNFR5 (SEQ ID No. 2) against the followingpublicly available databases: Arabidopsis (Arabidopsis thaliana,database maintained by the Carnegie Institution of Washington Departmentof Plant Biology); rice (Oryza sativa, database maintained by theInstitute for Genomic Research (TIGR)); poplar (Populus spp., databasemaintained by DOE's Joint Genome Institute); Medicago truncatula,database maintained by the lab of Nevin Young at the University ofMinnesota); and Lotus japonicus (database maintained by the Kazusa DNAResearch Institute in Japan. Domain structures of the resultingpotential LysM proteins were analyzed with Pfam software andInter-ProScan to identify LysM proteins. Soybean (Glycine max) LysMproteins were searched via tBLASTn (1e-5) using the same query sequencesas above against two publicly available EST databases, one maintained bythe Institute for Genomic Research, the other maintained by Monsanto.

Primers were designed based on the resulting soybean EST sequences toprobe a six-dimensional BAC pool for LysM-containing BACs via aPCR-based approach. The probed LYK-containing BACs were verified andshotgun sequenced to either finished phase (phase 3) at the ArizonaGenome Sequencing Center or prefinished phase (phase 2) at theWashington University Genome Sequencing Center. BAC sequences wereannotated using the dicot species model and Arabidopsis matrix ofFGENESH. Annotated proteins were similarly analyzed to screen for LYKproteins. Signal peptides and transmembrane domains were predicted withSignalP using both nearest-neighbor and hidden Markov model (HMM)algorithms and transmembrane HMM, respectively.

The GenBank accession numbers of soybean BACs are EF533702 forGMWb098N11; EF533695 for GMWb098N15; EF533696 for GMWb026N19; EF533701for GMWb095P01; EF533697 for GMWb035N07; EF533699 for GMWb069O12;EF533700 for GMWb080D08; and EF533698 for GMWb042124. LysM proteinsequences from species spanning all kingdoms were extracted from Pfamand searched for LysM motifs at an E-value cutoff of 0.1.

Sequence alignments were performed using ClustalX 1.83 (Thompson et al.,1997) with PHYLIP output format and edited in Jalview (Clamp et al.,2004). The average identities across the alignments for LysMe (type X),LysMn (type XI), and LYPb (type VII) were calculated based on theexported annotations in Jalview. An HMM profile calculated using hmmer(Eddy, 1998) for each alignment was used to realign (hmmalign) sequencesat matching states (−m) to identify and remove indel regions.

Parsimony trees were generated using the program protpars of PHYLIP(Felsenstein, 2000), with maximum-likelihood branch lengths calculatedusing TREE-PUZZLE (Schmidt et al., 2002). Distance trees were calculatedusing the program Protdist and Fitch of the PHYLIP package.Maximum-likelihood trees were calculated using the program proml of thePHYLIP package. Bootstrap values were calculated using the programseqboot of the PHYLIP package. Trees were viewed and rooted using A TreeViewer (Zmasek and Eddy, 2001). For calculation of nucleotidesubstitution rates, codon-aligned nucleic acid sequences were createdusing CodonAlign 2.0. All insertions and deletions were removed exceptthat a gap of more than 30 nucleotides was preferably retained todemonstrate the lack of the p loop and the activation loop in the kinasedomains of LjNFR5 orthologs (Limpens et al., 2003; Madsen et al., 2003;Arrighi et al., 2006). Nucleotide substitution levels were calculatedusing the program codeml of the PAML package (Yang, 1997) with auser-defined parsimony tree.

To build microsynteny maps, genomic sequences surrounding each LYK gene,about 0.5 to 0.9 Mb in length, were extracted from the above databasesand from soybean BAC sequences, which are about 100 to 170 kb in length.The genomic sequences were annotated using dicot species model andArabidopsis matrix of FGENESH for the five dicot plants and monocotspecies model and rice matrix for rice. The annotated protein sequenceswere compiled together into a peptide sequence database. Repetitivesequences were excluded from the databases. BLASTp was used to compareproteins against the database with an E-value cutoff of 1e-20 and apercent identity cutoff of 35% between species and 40% within samespecies and legumes. BLASTp results were then filtered once to removeretroelements. The microsynteny maps were finally drawn in AdobeIllustrator 10.0.

Example 2 Induction of Gene Expression in Arabidopsis Treated withChitin

A total of five LysM receptor-like kinase genes were identified inArabidopsis from the studies described in Example 1. The Genbank numbersof these five genes are AtLYK1 (GenBank accssion # At3g21630), AtLYK2(GenBank accssion # At3g01840), AtLYK3 (GenBank accssion # At1g51940),AtLYK4 (GenBank accssion # At2g23770), AtLYK5 (GenBank accssion #At2g33580), and, which are designated as SEQ ID. Nos. 3-7, respectively.A DNA microarray experiment was performed by treating Arabidopsis plantswith chitin. Leaves were treated by spraying with chitin (100 μM)+0.2%Tween-20. The Affymetrix 24K Arabidopsis genome chip was utilizedaccording to the manufacturer's instructions for this test. The dataobtained showed that transcription of 3 of the 5 Arabidopsis LysM RLKgenes, At2g33580 (13-fold), At3g21630 (2-fold) and At2g23770 (2-fold),was significantly increased by treating the plants with chitin. The dataimplicate these genes in plant chitin response.

Example 3 LysM RLK Mutants in Arabidopsis

To test whether non-leguminous LysM RLKs may be involved in theperception of chitooligosaccharides and the subsequent induction ofdownstream genes that have been implicated in fungal defense, T-DNAinsertion mutants were obtained for all five LysM RLK genes (i.e.,At1g51940, At2g23770, At2g33580, At3g01840, and At3g21630) inArabidopsis. The gene At3g21630 (SEQ ID. No. 3) is also termed AtLYK1 orAtLysM RLK1. Homozygous mutants were then treated with a purifiedchitooligosaccharide (chitooctaose) and the expression levels of knownCRGs, such as MPK3 (At3g45640, SEQ ID. No. 8), WRKY22 (At4g01250, SEQID. No. 9), WRKY29 (At4g23550, SEQ ID. No. 10), WRKY33 (At2g38470, SEQID. No. 11), and WRKY53 (At4g23810, SEQ ID. No. 12), were measured.

More particularly, Arabidopsis seedlings were grown hydroponically asdescribed by Ramonell et al., 2005. Fourteen-day old seedlings weretreated with chitooctaose (Sigma, St. Louis, Mo., USA) at aconcentration of 1 μM or with distilled water (as a control) for 30minutes. To test flagellin-responsive genes, 14-day old seedlings werealso treated with the flagellinderived flg22 peptide (dissolved indimethyl sulfoxide, DMSO) at a final concentration of 10 μM or with anequivalent amount of DMSO (as a control) for 30 minutes. To test otherdefense pathways, Arabidopsis seedlings were also treated for 24 hourswith 5 mM SA, 100 μM MeJA, and 0.5 mM ACC (all obtained from Sigma, St.Louis, Mo., USA) and dissolved in 0.1% ethanol. The control plants weresimilarly treated with an equivalent amount of ethanol. After treatment,the seedlings were collected and frozen in liquid nitrogen for RNAisolation.

Total RNA was isolated using the Trizol Reagent according to themanufacturer's instructions (Invitrogen, Carlsbad, Calif.). The isolatedRNA was further purified using Qiagen RNeasy Mini Columns according tothe manufacturer's instruction (Qiagen, Valencia, Calif., USA) andtreated with Turbo™ DNase (Ambion, Austin, Tex., USA). Forsemi-quantitative RT-PCR or quantitative 17 PCR, cDNA was synthesizedusing M-MLV reverse transcriptase according to the manufacturer'sinstructions (Promega, Madison, Wis., USA).

Semi-Quantitative RT-PCR.

The gene-specific primer pairs (forward and reverse) for detecting thefollowing selected chitooligosaccharide-responsive genes (CRGs) are:

For MPK3 (At3g45640): (SEQ ID No. 13) 5′-CTCACGGAGGACAGTTCATAAG-3′ and(SEQ ID No. 14) 5′-GAGATCAGATTCTGTCGGTGTG-3′ For WRKY22 (At4g01250):(SEQ ID No. 15) 5′-GTAAGCTCATCAGCTACTACCAC-3′ and (SEQ ID No. 16)5′-ACCGCTAGATGATCCTCAACAG-3′ for WRKY29 (At4g23550): (SEQ ID No. 17)5′-ATGGACGAAGGAGACCTAGAAG-3′ and (SEQ ID No. 18)5′-CCGCTTGGTGCGTACTCGTTTC-3′ For WRKY33 (At2g38470): (SEQ ID No. 19)5′-CTCCGACCACAACTACAACTAC-3′ and (SEQ ID No. 20)5′-GGCTCTCTCACTGTCTTGCTTC-3′ For WRKY53 (At4g23810): (SEQ ID No. 21)5′-CCTACGAGAGATCTCTTCTTCTG-3′ and (SEQ ID No. 22)5′-AGATCGGAGAACTCTCCACGTG-3′

As an internal control, the following forward and reverse primers ofactin-2 (At3g18780) were included in the same PCR reaction with eachprimer pair of the above genes:

(SEQ ID No. 23) 5′-GACTAAGAGAGAAAGTAAGAGATAATCCAG-3′ and (SEQ ID No. 24)5′-CAGCCTTTGATTTCAATTTGCATGTAAGAG-3′.

PCR reactions were conducted using Taq polymerase (Promega, Madison,Wis., USA) under the following conditions: 94° C., 3 minutes; 94° C., 30seconds; 55° C., 30 seconds; 72° C., 1.5 minutes; 25 cycles; 72° C., 3minutes. The corresponding CRG genes in Lotus japonicus were identifiedby blasting the cDNA sequences of the above Arabidopsis CRGs (and alsoactin-2) against the TIGR Lotus japonicus Gene Index. The closest hitswere chosen and arbitrarily named after their Arabidopsis counterpartswith the prefix Lj (standing for Lotus japonicus). The following primerpairs were designed to detect these genes:

For LjMPK3 (TC8079): (SEQ ID No. 25)5′-CACCCTTGCGTAGAGAGTTTACTGATGTC-3′, and (SEQ ID No. 26)5′-GTTGACGAGGATATTGAGGAAGTTGTCTG-3′; For LjWRKY22 (AV423663):(SEQ ID No. 27) 5′-TCACCTTGCTGGTTCTGGTTCTGGTTCTG-3′, and (SEQ ID No. 28)5′-TCTGATAGGGGTGCAACCCCATCTTCTTC-3′; For LjWRKY33 (TC14849):(SEQ ID No. 29) 5′-AGTTGTGGTTCAGACCACCAGTGACATTG-3′ and (SEQ ID No. 30)5′-ACCCCATTGAGTTTCCAAACCCTGATGAG-3′; For LjWRKY53 (TC9074):(SEQ ID No. 31) 5′-CCCATCAAAAGAACCAACCACAACAAGAG-3′ and (SEQ ID No. 32)5′-ATCCGCACGCACTTGAACCATGTATTGTG-3′; For LjActin-2 (TC14247):(SEQ ID No. 33) 5′-AAGGTTCGTAAACGATGGCTGATGCTGAG-3′ and (SEQ ID No. 34)5′-ACCTTGATCTTCATGCTGCTAGGAGCAAG-3′.

LjActin-2 was used as an internal control.

Quantitative PCR.

To quantify gene expression using quantitative PCR, the forward andreverse primers of each gene were as follows:

For PR-1 (At2g14610, SEQ ID. No. 35): (SEQ ID No. 36)5′-AACACGTGCAATGGAGTTTGTGGTCACT-3′ and (SEQ ID No. 37)5′-ACCATTGTTACACCTCACTTTGGCACAT-3′;For PDF1.2 (At5g44420, SEQ ID. No. 38): (SEQ ID No. 39)5′-AGTGCATTAACCTTGAAGGAGCCAAACAT-3′ and (SEQ ID No. 40)5′-AACAGATACACTTGTGTGCTGGGAAGACA-3′; For MPK3 (At3g45640):(SEQ ID No. 41) 5′-TGGCCATTGATCTTGTTGACAGAATGTTGA-3′ and (SEQ ID No. 42)5′-TCGTGCAATTTAGCAAGGTACTGGTGATT-3′; for WRKY53 (At4g23810):(SEQ ID No. 43) 5′-TTTAGGCGCCAAATTCCCAAGGAGTTATT-3′ and (SEQ ID No. 44)5′-TCTGGACTTGTTTCGTTGCCCAACAGTTT-3′; For actin-2 (At3g18780):(SEQ ID No. 45) 5′-GGTATTCTTACCTTGAAGTATCCTATTG-3′ and (SEQ ID No. 46)5′-CTCATTGTAGAAAGTGTGATGCCAGATC-3′.

Actin-2 was used as an internal control to normalize gene expressionacross different samples. The reactions were conducted on a 7500Real-Time PCR System (Applied Biosystems, Foster City, Calif., USA)using the SYBR®Green Master Mix (Applied Biosystems, Foster City,Calif., USA) with the following PCR conditions: 95° C., 10 minutes; 95°C., 15 seconds; 60° C., 1 minute; 40 cycles; followed by thedissociation curve analysis to verify single amplicon. The fold changein the target gene, normalized to actin-2 and relative to the geneexpression in the control sample, was calculated as described inRamonell et al., 2002.

The AtLysM RLK1 insertion mutant (096F09) used in the current work wasgenerated in the context of the GABI-Kat program and provided by BerndWeisshaar (MPI for Plant Breeding Research, Cologne, Germany) SeeShibuya et al., 2001. The homozygous plants were identified bygenotyping using the following gene-specific primers:

(SEQ ID No. 47) 5′- AGAATATATCCACGAGCACACGGTTCCAG-3′ (forward), and(SEQ ID No. 48) 5′-GACGAAAAGAGAGTGGATAAAGCAACCAC-3′ (reverse)together with the T-DNA left border primer: (SEQ ID No. 49)5′-CCCATTTGGACGTGAATGTAGACAC-3′.

These two primers were also used to detect the expression of the AtLysMRLK1 gene via RT-PCR. The other primers used to detect the transcript 5′of the insertion site were as follows:

(SEQ ID No. 50) 5′-ATGAAGCTAAAGATTTCTCTAATCGCTC-3′, and (SEQ ID No. 51)5′-GAAATGCACCATTTGGATCTCTTCCAG-3′

The mutants of the other 4 Arabidopsis LysM RLK genes were obtained fromthe SALK Institute and Syngenta Incorporation through the ArabidopsisBasic Research Center (ABRC) or from the Martienssen lab at the ColdSpring Harbor Laboratory.

One insertion mutant designated as L3 with an insertion in geneAt1g51940 exhibited an interesting phenotype. This mutant showedenhanced expression of some defense-related genes, such as PR-2 andPR-1, as shown in FIG. 3. The PR-2 gene (AT3G57260, SEQ ID. No. 52)encodes a β-1,3-glucanase, which is an enzyme that degrades the fungalcell wall component glucan to inhibit fungal infection. PR-1 (SEQ ID.No. 35) has also been shown to be involved in plant defense againstpathogens, especially bacterial pathogens. This enhanced expression ofdefense genes suggests that the mutant may be resistant to fungalpathogens. The test of this mutant with a fungal pathogen calledBotrytis cinerea demonstrated that the mutant is resistant to thisfungal pathogen, as shown in FIG. 4A. B. cinerea is a necrotrophicfungus, and dead plants were assessed as those having no remaininggreen, only yellowish leaves. The L3 mutant demonstrated increasedresistance relative to the wild-type plant.

In addition, the L3 mutant showed decreased susceptibility to thebacterial pathogen Pseudomonas syringae strain DC3000, as shown in FIG.4B. The enhanced resistance is likely due to the knockout of thespecific LysM receptor kinase gene. Analysis of expression of theAt1g51940 gene in the L3 mutant failed to detect the mRNA. Therefore,the lack of At1g51940 gene expression correlates with elevated PR1expression and enhanced disease resistance. This suggests that At1g51940may act normally to repress the disease resistance response according toa model pathway of the involvement of the LYSM RK in plant defense, asshown in FIG. 5. Therefore, it is possible to make plants more resistantto fungal pathogens by either knocking out or knocking down theexpression of this gene. Furthermore, dominant negative forms of thisprotein may also be made and employed to modulate plant fungalresistance.

Another insertion mutant, corresponding to At3g21630, or AtLYK1(designated hereafter as AtLysM RLK1), almost completely blocked theinduction of all the selected CRGs (FIG. 6A), suggesting a critical roleof AtLysM RLK1 in the perception of chitooligosaccharides. Both themutant (Mu) and wildtype (WT) plants were treated with purifiedchitooctaose or water (as a control) for 30 minutes and gene expressionof the selected CRGs was detected using semi-quantitative RT-PCR.Actin-2 was used as an internal control. The amplification of bothactin-2 and a CRG was conducted in the same tube.

The AtLysM RLK1 gene (SEQ ID. No. 3) is 2988 nucleotides (nts) long,with 11 introns (FIG. 6B) and a coding sequence of 1854 nts. Squareboxes represent exons. Solid lines between them are introns. The startcodon (ATG) and stop codon (TAG) are included in the first and lastexon, respectively. The two T-DNA insertions (T-DNA1 and 2) inserted inthe 10th intron in the AtLysM RLK1 mutant are indicated above the gene.LB: left border; RB: right border. The AtLysM RLK1 gene encodes a LysMRLK of 617 amino acids (SEQ ID No. 53), with an extracellular domain(containing 3 predicted LysM motifs), a transmembrane domain (TM), andan intracellular serine/threonine kinase domain. FIG. 6C illustrates thepredicted domain structure of AtLysM RLK1. S: signal peptide; LysM: LysMdomain; TM: transmembrane domain; Ser/Thr Kinase: Serine/Threoninekinase domain. AtLysM RLK1 has been shown to be phylogenetically relatedto the Nod signal receptor NFR1. Zhang et al., 2007.

Two T-DNA insertions were identified in the AtLysM RLK1 mutant,separated by 4 nts, in the 10th intron (FIG. 6B). RT-PCR analysis usingprimers corresponding to the exon regions on the side of the 10th intronfailed to detect mRNA expression in the AtLysM RLK1 mutant; however, atruncated transcript derived from the gene sequence before the intronwas detected by RT-PCR (FIGS. 7A and 7B), suggesting the T-DNAinsertions in the intron blocked full-length transcription of the gene.

To confirm that the observed changes in CRGs expression were caused bythe mutation in the AtLysM RLK1 gene, the mutant was complemented withthe full-length AtLysM RLK1 cDNA driven by the constitutive CauliflowerMosaic Virus (CMV) 35S promoter. More specifically, the full-length CDS(1854 nucleotides long) was obtained by RT-PCR and cloned in the Eco RVsite of the pBluescript vector. The confirmed sequence was furthercloned into the modified binary 16 vector pCAMBIA1200 that contains a35S promoter-Multiple Cloning Sites (MCS)-poly A signal, downstream ofthe 35S promoter. The final construct was electroporated intoAgrobacterium tumafaciens EHA105 according to the procedures describedby Stacey and Shibuya, 1997. The resultant A. tumafaciens was then usedto transform the homozygous AtLysM RLK1 mutant via floral dipping asdescribed by Passarinho et al., 2002.

Multiple transgenic lines were obtained. The complemented plants weretreated with chitooctaose or water (as a control) at a finalconcentration of 1 μM for 30 minutes. RT-PCR data show that the selectedCRGs were induced to a level in the selected complemented plants (Com-1and Com-2) similar to the level in the wild type (WT) plants (FIG. 8).Com-1 and Com-2 are two independent complemented lines and WT iswild-type Col-0 plants.

Thus, the complemented plants showed restored induction of thoseselected CRGs, confirming that it was the insertions in the AtLysM RLK1gene that caused the observed change in gene expression. Thecomplementation data also ruled out the possibility that a truncatedprotein translated from the observed truncated transcript may haveaffected the expression of the selected CRGs.

The expression pattern of the AtLysM RLK1 gene was also studied. RT-PCRdata show that AtLysM RLK1 is expressed ubiquitously in the whole plant,in tissues such as root, rosette leaf, cauline leaf, stem,inflorescence, silique, flower bud, open flower, and pollen, with thelowest expression levels in pollen (FIG. 9). Interestingly, this genewas induced by chitooligosaccharides, but not by the flg22 peptidederived from flagellin, a PAMP (pathogen-associated molecular pattern)produced by pathogenic bacteria (FIG. 10) (Gomez-Gomez et al., 2000),suggesting a specific role of this gene in chitooligosaccharidesignaling. More specifically, for experiment (A), fourteen-day-old,hydroponically grown seedlings were treated for 30 minutes withchitooctaose at a final concentration of 1 μM or with distilled water(as a control); for experiment (B), the seedlings were treated withflg22 (dissolved in DMSO) at a final concentration of 10 μM or with anequivalent amount of DMSO (as a control).

Gene expression profiles in the AtLysM RLK1 mutant in response tochitooctaose were studied using the Affymetrix Arabidopsis Whole GenomeArray ATH1 (with ˜22000 genes), with wild-type plants as a control. Dataanalysis showed that a total of 909 genes responded more than 1.5 fold(P<0.05) to chitooctaose elicitation in both the wild-type and mutantplants 30 minutes after the treatment (FIG. 11A). A row represents agene and each column represents a sample. WT-8mer=wild-type Col-0treated with chitooctaose; WT-water=wild-type Col-0 treated withdistilled water; Mu-water=the AtLysM RLK1 mutant treated with distilledwater; Mu-8mer=the AtLysM RLK1 mutant treated with chitooctaose. Thecolor bar below the cluster picture: the red color indicates theexpression level of a gene is above the mean expression of the geneacross all samples; the green color indicates expression lower than themean. These genes can be separated into two groups: up- anddown-regulated by chitooctaose, as represented by the two large clustersin FIG. 11A.

Out of the 909 genes tested, 890 showed a change in transcript levels inthe wild-type plants in response to chitooctaose, with 663 up-regulatedand 227 down-regulated (FIG. 11B, 11C and Table 3). Up-regulated genes:1.5 fold, P<0.05. Down-regulated genes: 1.5 fold, P<0.05. By contrast,only 33 genes out of 909 were responsive in the mutant, with 16up-regulated and 17 down-regulated (FIGS. 11B and 11C; Table 4). Amongthe 33 genes, 14 genes (3 up- and 11 down-regulated) were also similarlyregulated in the wild-type plants (rows 1 to 15 in Table 4), leavingonly 19 genes that appeared to be differentially regulated bychitooctaose in the mutant (rows 16-34 in Table 4). However, 13 of thesegenes showed a similar regulation trend (up- or down-regulation) in thewild-type plants to that in the mutant, although such a trend was notconsidered significant in the wild-type plants (rows 16 to 28 in Table4).

TABLE 3 Genes that are Responsive to chitooctaose in Wild-type WT MuProbe set Annotation Accession FC FC WT P Mu P 245613_at hypotheticalprotein At4g14450 72.79 −1.8 0.019018 0.836714 249197_at putativeprotein contains similarity to At5g42380 51.63 1.06 0.019359 0.866994calmodulin; supported by full-length cDNA: Ceres: 99348. 258947_athypothetical protein similar to calmodulin-like At3g01830 43.33 1.580.012148 0.103554 protein GB: CAB42906 [Arabidopsis thaliana]; Pfam HMMhit: EF hand; supported by full-length cDNA: Ceres: 7252. 260399_atputative lipoxygenase similar to lipoxygenase At1g72520 41.48 −1.110.009183 0.804844 GB: CAB56692 [Arabidopsis thaliana]; supported bycDNA: gi_15810254_gb_AY056166.1_(—) 257540_at hypothetical proteinAt3g21520 34.95 1.08 0.001687 0.921695 256526_at disease resistanceprotein, putative similar to disease At1g66090 33.68 −1.13 0.016280.597847 resistance protein RPP1-WsA [Arabidopsis thaliana] GI: 3860163;supported by full-length cDNA: Ceres: 93530. 250796_at putative proteinsimilar to unknown protein At5g05300 31.56 1.1 0.004167 0.773037(gb|AAF01528.1) 261474_at anionic peroxidase, putative similar toanionic At1g14540 30.96 −1.02 0.001414 0.955549 peroxidase GI: 170202from [Nicotiana sylvestris] 245755_at hypothetical protein predicted byAt1g35210 30.5 −1.11 0.01789 0.881393 genemark.hmm; supported byfull-length cDNA: Ceres: 42217. 254231_at putative proteinAR411-Arabidopsis thaliana (thale At4g23810 28.21 −1.25 0.0184010.425568 cress), PID: g1669603; supported by cDNA:gi_13507100_gb_AF272748.1_AF272748 248322_at putative protein similar tounknown protein At5g52760 26.14 1.31 0.004693 0.152597 (emb|CAA71173.1)249770_at unknown protein; supported by full-length cDNA: At5g2411025.43 −1.06 0.035483 0.869658 Ceres: 6469. 247215_at Expressed protein;supported by full-length cDNA: At5g64905 24.84 1.24 0.04883 0.449026Ceres: 3657. 265725_at putative alanine acetyl transferase At2g3203023.73 1.08 0.027584 0.473742 266821_at putative ethylene responseelement binding protein At2g44840 23.69 −1.22 0.019899 0.271281 (EREBP);supported by full-length cDNA: Ceres: 6397. 248904_at Expressed protein;supported by full-length cDNA: At5g46295 23.69 −1.49 0.007953 0.428724Ceres: 18973. 261648_at salt-tolerance zinc finger protein identical tosalt- At1g27730 22.71 −1.09 0.016239 0.33423 tolerance zinc fingerprotein GB: CAA64820 GI: 1565227 from [Arabidopsis thaliana]; supportedby cDNA: gi_14334649_gb_AY034998.1_(—) 262085_at hypothetical proteinpredicted by genemark.hmm At1g56060 22.37 1.36 0.001015 0.285112261021_at hypothetical protein similar to reticuline oxidase-likeAt1g26380 22.2 2.37 0.004697 0.108353 protein GB: CAB45850 GI: 5262224from [Arabidopsis thaliana]; supported by cDNA:gi_13430839_gb_AF360332.1_AF360332 263182_at Expressed protein;supported by full-length cDNA: At1g05575 19.34 −1.02 0.005652 0.804382Ceres: 27081. 249417_at calcium-binding protein-like cbp1calcium-binding At5g39670 18.84 −1.03 0.012777 0.874622 protein, Lotusjaponicus, EMBL: LJA251808; supported by cDNA:gi_16648829_gb_AY058192.1_(—) 254120_at putative mitochondrialuncoupling protein At4g24570 18.47 −1.26 0.006894 0.121685 mitochondrialuncoupling protein, Arabidopsis thaliana (thale cress), PATX: E1316826;supported by full-length cDNA: Ceres: 119476. 264153_at diseaseresistance protein RPS4, putative similar to At1g65390 17.77 −1.010.006757 0.837017 disease resistance protein RPS4 GI: 5459305 from[Arabidopsis thaliana] 249264_s_at disease resistance protein-likeAt5g41740 17.16 1.01 0.016032 0.965149 246821_at calmodulin-binding-likeprotein calmodulin- At5g26920 16.58 −1.22 0.002033 0.305516 bindingprotein TCB60, Nicotiana tabacum, EMBL: U58971 265327_at unknown proteinAt2g18210 16.02 −1.08 0.007312 0.847704 252131_at BCS1 protein-likeprotein Homo sapiens h-bcs1 At3g50930 15.81 1.28 0.020727 0.19657 (BCS1)mRNA, nuclear gene encoding mitochondrial protein which is involved inthe expression of functional mitochondrial ubiquinol- cytochrome creductase complex probably via the control of expression of Riesk245840_at hypothetical protein predicted by At1g58420 15.76 −1.160.001929 0.649675 genemark.hmm; supported by full-length cDNA: Ceres:124269. 245041_at AR781, similar to yeast pheromone receptor At2g2653015.71 −1.4 0.011514 0.105739 identical to GB: D88743, corrected aframeshift found in the original record (at 69530 bp), sequencesubmitted has been verified from 10 sequence electropherograms. Thetranslation now starts from an upstream ATG. 248799_at ethyleneresponsive element binding factor 5 At5g47230 15.6 −1.36 0.0052080.117072 (ATERF5) (sp|O80341); supported by cDNA:gi_14326511_gb_AF385709.1_AF385709 250149_at cinnamoyl CoAreductase-like protein cinnamoyl At5g14700 15.46 −1.13 0.022877 0.554222CoA reductase, Populus tremuloides, EMBL: AF217958; supported byfull-length cDNA: Ceres: 17229. 256306_at lipase, putative contains Pfamprofile: PF01764: At1g30370 15.3 1.11 0.00866 0.751633 Lipase 246777_atRING-H2 zinc finger protein-like RING-H2 zinc At5g27420 14.67 −1.440.011803 0.037951 finger protein ATL6-Arabidopsis thaliana, EMBL:AF132016; supported by full-length cDNA: Ceres: 106078. 263783_atputative WRKY-type DNA binding protein; At2g46400 14.41 1.26 0.0055890.126494 supported by cDNA: gi_15430276_gb_AY046275.1_(—) 245369_atExpressed protein; supported by full-length cDNA: At4g15975 14.34 1.030.00366 0.920236 Ceres: 124835. 251336_at putative protein hypotheticalprotein F4I18.26- At3g61190 14.31 1.07 0.007665 0.724447 Arabidopsisthaliana, PIR: T02471; supported by full- length cDNA: Ceres: 30454.260046_at Expressed protein; supported by cDNA: At1g73800 13.55 10.010217 0.9771 gi_16648699_gb_AY058126.1_(—) 260068_at putativecalmodulin-binding protein similar to At1g73805 13.35 1.16 0.0073830.51944 calmodulin-binding protein GB: AAB37246 [Nicotiana tabacum]266071_at unknown protein At2g18680 13.32 1.11 0.004216 0.713949253643_at hypothetical protein; supported by full-length At4g29780 13.05−1.11 0.002383 0.344174 cDNA: Ceres: 249769. 264213_at hypotheticalprotein contains similarity to lectin At1g65400 12.76 −1.17 0.0214980.255697 polypeptide GI: 410436 from [Cucurbita maxima] 262382_at virusresistance protein, putative similar to virus At1g72920 12.68 −1.40.003189 0.073493 resistance protein GI: 558886 from [Nicotianaglutinosa] 247543_at DNA binding protein-like DNA binding proteinAt5g61600 12.31 −1.31 0.014862 0.112814 EREBP-4, Nicotiana tabacum, PIR:T02434; supported by full-length cDNA: Ceres: 92102. 256442_athypothetical protein predicted by At3g10930 11.62 −1.07 0.0252880.782271 genefinder; supported by full-length cDNA: Ceres: 12509.253060_at putative protein predicted protein, Arabidopsis At4g3771011.56 1.34 0.005721 0.412461 thaliana; supported by full-length cDNA:Ceres: 207350. 253915_at putative protein centrin, Marsilea vestita;supported At4g27280 11.5 −1.07 0.01185 0.333253 by full-length cDNA:Ceres: 13072. 249928_at CCR4-associated factor-like protein At5g2225011.41 −1.17 0.009043 0.204172 245711_at putative c2h2 zinc fingertranscription factor At5g04340 11.35 −1.11 0.016673 0.392119 261892_attranscription factor, putative similar to WRKY At1g80840 11.27 1.090.006954 0.498704 transcription factor GB: BAA87058 GI: 6472585 from[Nicotiana tabacum]; supported by full-length cDNA: Ceres: 6437.261394_at wall-associated kinase 2, putative similar to wall- At1g7968011.05 1.08 0.003074 0.819188 associated kinase 2 GI: 4826399 from[Arabidopsis thaliana] 251774_at nematode resistance protein-likeprotein Hs1pro-1 At3g55840 11.02 −1.37 0.007795 0.481526 nematoderesistance gene, Beta procumbens, EMBL: BPU79733; supported byfull-length cDNA: Ceres: 149697. 265723_at putative disease resistanceprotein At2g32140 10.99 1.18 0.016981 0.537825 255339_at hypotheticalprotein similar to A. thaliana At4g04480 10.83 1.32 0.012367 0.514455hypothetical protein F1N20.130, GenBank accession number AL022140251054_at receptor like protein kinase receptor like protein At5g0154010.66 −1.01 0.003949 0.917593 kinase-Arabidopsis thaliana, EMBL:ATLECGENE; supported by cDNA: gi_13605542_gb_AF361597.1_AF361597253827_at Expressed protein; supported by cDNA: At4g28085 10.37 −1.090.010797 0.530514 gi_15028040_gb_AY045877.1_(—) 255945_at putativeprotein At5g28610 10.06 1.21 0.010366 0.464865 249618_at putativeprotein predicted proteins, Arabidopsis At5g37490 9.99 −1.09 0.0047190.814525 thalina 248934_at serine/threonine protein kinase-like proteinAt5g46080 9.94 −1.17 0.007605 0.645509 261037_at lipoxygenase identicalto GB: CAB56692 from At1g17420 9.88 −1.1 0.002351 0.775492 (Arabidopsisthaliana) 267623_at unknown protein At2g39650 9.87 −1.12 0.0067440.439834 259428_at MAP kinase, putative similar to MAP kinase 5At1g01560 9.84 1.54 0.002458 0.135149 GI: 4239889 from [Zea mays]246927_s_at nodulin-like protein nodulin, Glycine max, At5g25260 9.741.6 0.004623 0.163075 EMBL: AF065435 264758_at late embryogenesisabundant protein, putative At1g61340 9.73 1.17 0.016626 0.389155 similarto late embryogenesis abundant protein GI: 1350540 from [Picea glauca]245329_at Expressed protein; supported by full-length cDNA: At4g143659.7 1.42 0.002486 0.029582 Ceres: 37809. 262072_at hypothetical proteinpredicted by At1g59590 9.54 −1.12 0.009452 0.599212 genemark.hmm;supported by full-length cDNA: Ceres: 99553. 255844_at putative proteinkinase contains a protein kinase At2g33580 9.42 1.11 0.006611 0.553845domain profile (PDOC00100) 253632_at senescence-associated proteinhomolog senescence- At4g30430 9.29 1.22 0.004184 0.351697 associatedprotein 5-Hemerocallis hybrid cultivar, PID: g3551954; supported byfull-length cDNA: Ceres: 122632. 257511_at hypothetical proteinAt1g43000 9.29 −1.13 0.020984 0.846669 253999_at1-aminocyclopropane-1-carboxylate synthase-like At4g26200 9.24 −1.560.004129 0.115048 protein ACC synthase, Malus domestica, U73816265920_s_at unknown protein At2g15120 9.13 1.33 0.001682 0.33404263800_at hypothetical protein predicted by genscan; supported At2g246008.97 1.02 0.014457 0.769925 by cDNA: gi_15810330_gb_AY056204.1_(—)248164_at putative protein similar to unknown protein At5g54490 8.97−1.17 0.008767 0.190232 (pir||T05752); supported by full-length cDNA:Ceres: 109272. 265597_at Expressed protein; supported by cDNA: At2g201458.96 −1 0.023429 0.965819 gi_13605516_gb_AF361584.1_AF361584 248327_atputative protein similar to unknown protein At5g52750 8.93 −1.040.017097 0.808905 (emb|CAA71173.1); supported by full-length cDNA:Ceres: 19542. 252908_at putative protein At4g39670 8.56 1.17 0.0126610.466742 251400_at putative protein prib5, Ribes nigrum, At3g60420 8.531.64 0.029245 0.023237 EMBL: RNI7578; supported by full-length cDNA:Ceres: 31361. 261475_at anionic peroxidase, putative similar to anionicAt1g14550 8.51 1.41 0.01103 0.395333 peroxidase GI: 170202 from[Nicotiana sylvestris] 256185_at dof zinc finger protein identical todof zinc finger At1g51700 8.47 −1.09 0.001565 0.51485 protein[Arabidopsis thaliana] GI: 3608261; supported by cDNA:gi_3608260_dbj_AB017564.1_AB017564 250493_at putative protein variouspredicted proteins, At5g09800 8.28 −1.06 0.010787 0.857557 Arabidopsisthaliana 252679_at CCR4-associated factor 1-like protein At3g44260 8.27−1.27 0.000484 0.065446 CAF1_MOUSE CCR4-ASSOCIATED FACTOR 1- Musmusculus, SWISSPROT: CAF1_MOUSE; supported by cDNA:gi_15292828_gb_AY050848.1_(—) 265797_at Expressed protein; supported byfull-length cDNA: At2g35715 8.26 −1.27 0.005817 0.60028 Ceres: 9996.248448_at putative protein contains similarity to ethylene At5g511908.25 −1.1 0.009635 0.575899 responsive element binding factor; supportedby full- length cDNA: Ceres: 2347. 255884_at hypothetical proteinpredicted by At1g20310 8.15 −1.19 0.022852 0.204061 genemark.hmm;supported by full-length cDNA: Ceres: 8562. 261449_at putative ATPasesimilar to GB: AAF28353 from At1g21120 7.97 1.46 0.004955 0.182958[Fragaria × ananassa] 265841_at putative glycogenin At2g35710 7.96 −1.270.011587 0.280483 251895_at class IV chitinase (CHIV) At3g54420 7.95−1.09 0.003142 0.722712 263935_at unknown protein At2g35930 7.89 −1.060.006185 0.342267 255502_at contains similarity to a protein kinasedomain (Pfam: At4g02410 7.89 −1.07 0.003365 0.691648 pkinase.hmm, score:166.20) and to legume lectins beta domain (Pfam: lectin_legB.hmm, score:139.32) 258787_at hypothetical protein predicted by genscan; supportedAt3g11840 7.84 −1.13 0.036463 0.37994 by full-length cDNA: Ceres:100676. 266658_at Expressed protein; supported by full-length cDNA:At2g25735 7.71 −1.47 0.003942 0.026409 Ceres: 7152. 245250_at ethyleneresponsive element binding factor-like At4g17490 7.54 1.06 0.0082420.704323 protein (AtERF6); supported by cDNA:gi_3298497_dbj_AB013301.1_AB013301 247487_at putative protein predictedprotein, Arabidopsis At5g62150 7.39 1.01 0.005388 0.945249 thaliana261470_at ethylene-responsive element binding factor, putative At1g283707.33 −1.17 0.005528 0.478834 similar to ethylene-responsive elementbinding factor GI: 8809573 from [Nicotiana sylvestris]; supported byfull-length cDNA: Ceres: 27635. 262381_at virus resistance protein,putative similar to virus At1g72900 7.27 −1.19 0.006528 0.311035resistance protein GI: 558886 from [Nicotiana glutinosa] 248123_atputative protein similar to unknown protein At5g54720 7.23 1.29 0.0062140.245803 (gb|AAD32884.1) 263379_at putative CCCH-type zinc fingerprotein also an At2g40140 7.21 1.01 0.004911 0.848966 ankyrin-repeatprotein 263584_at NAM (no apical meristem)-like protein similar toAt2g17040 7.13 −1.29 0.006099 0.12014 petunia NAM (X92205) and A.thaliana sequences ATAF1 (X74755) and ATAF2 (X74756); probableDNA-binding protein; supported by cDNA:gi_13605646_gb_AF361804.1_AF361804 259566_at hypothetical proteinAt1g20520 7.04 −1.14 0.024145 0.734624 267028_at putative WRKY-type DNAbinding protein At2g38470 7.02 −1.19 0.009642 0.27064 265008_at Mloprotein, putative similar to Mlo protein At1g61560 6.99 1.2 0.002980.470024 GI: 1877220 from [Hordeum vulgare]; supported by cDNA:gi_14091581_gb_AF369567.1_AF369567 247693_at putative protein leucinezipper-containing protein, At5g59730 6.97 1.01 0.004438 0.963142Lycopersicon esculentum, PIR: S21495; supported by cDNA:gi_14334437_gb_AY034910.1_(—) 257748_at hypothetical protein predictedby genemark.hmm At3g18710 6.82 −1.16 0.009082 0.446456 258351_athypothetical protein contains similarity to ion At3g17700 6.78 −1.020.004386 0.920019 channel protein from [Arabidopsis thaliana]; supportedby cDNA: gi_8131897_gb_AF148541.1_AF148541 251745_at putative proteinzinc finger transcription factor At3g55980 6.71 −1.36 0.001393 0.169064(PEI1), Arabidopsis thaliana, EMBL: AF050463; supported by cDNA:gi_15810486_gb_AY056282.1_(—) 257536_at unknown protein At3g02800 6.461.24 0.011172 0.244827 246108_at putative protein retinal glutamicacid-rich protein, At5g28630 6.43 −1.14 0.017801 0.374617 bovine, PIR:A40437; supported by full-length cDNA: Ceres: 24151. 256046_at unknownprotein At1g07135 6.42 −1.28 0.005287 0.339032 258436_at putative RINGzinc finger protein similar to RING- At3g16720 6.39 −1.2 0.0025250.290143 H2 zinc finger protein ATL6 GB: AAD33584 from [Arabidopsisthaliana]; supported by full-length cDNA: Ceres: 4581. 254255_atserine/threonine kinase-like protein At4g23220 6.39 1.58 0.011570.225448 serine/threonine kinase, Brassica oleracea; supported by cDNA:gi_14423417_gb_AF386946.1_AF386946 248686_at 33 kDa secretoryprotein-like; supported by cDNA: At5g48540 6.37 1.07 0.007302 0.530534gi_15292980_gb_AY050924.1_(—) 248726_at RAS superfamily GTP-bindingprotein-like; At5g47960 6.34 −1 0.011505 0.996984 supported by cDNA:gi_12004622_gb_AF218121.1_AF218121 256633_at unknown protein At3g283406.32 −1.23 0.013314 0.277616 256183_at MAP kinase kinase 4 (ATMKK4)identical to MAP At1g51660 6.32 1.03 0.001255 0.842274 kinase kinase 4[Arabidopsis thaliana]; supported by cDNA:gi_13265419_gb_AF324667.2_AF324667 247949_at cytochrome P450 At5g572206.31 −1.03 0.00798 0.740555 250098_at putative protein; supported byfull-length cDNA: At5g17350 6.21 −1.09 0.005623 0.628534 Ceres: 1198.255504_at drought-induced-19-like 1 similar to drought- At4g02200 6.141.1 0.002902 0.428306 induced-19, GenBank accession number X78584similar to F2P16.10, GenBank accession number 2191179 identical toT10M13.20 253414_at putative protein At4g33050 6.08 −1.1 0.0020730.284317 262731_at hypothetical protein similar to gb|AF098458 latex-At1g16420 6.07 1.18 0.016528 0.727417 abundant protein (LAR) from Heveabrasiliensis 247848_at resistance protein-like disease resistanceprotein At5g58120 6.07 −1.04 0.01295 0.876046 RPP1-WsA, Arabidopsisthaliana, EMBL: AF098962 254926_at ACC synthase (AtACS-6); supported bycDNA: At4g11280 6.04 −1.17 0.005123 0.161176gi_16226285_gb_AF428292.1_AF428292 249719_at Expressed protein;supported by full-length cDNA: At5g35735 6.04 −1.08 0.005081 0.233393Ceres: 32450. 247208_at nodulin-like; supported by full-length cDNA:At5g64870 6.04 1.22 0.001605 0.225756 Ceres: 142026. 257478_athypothetical protein similar to putative At1g16130 5.96 −1.23 0.0089180.562604 serine/threonine-specific protein kinase GI: 7270012 from[Arabidopsis thaliana] 246993_at Cys2/His2-type zinc finger protein 1At5g67450 5.95 −1.06 0.005299 0.855156 (dbj|BAA85108.1) 252060_atputative protein other hypothetical proteins in At3g52430 5.94 1.20.005073 0.34486 Arabidopsis thaliana; supported by cDNA:gi_6457330_gb_AF188329.1_AF188329 267381_at unknown protein; supportedby cDNA: At2g26190 5.9 −1.09 0.006528 0.587987gi_16930468_gb_AF419588.1_AF419588 245038_at similar to latex allergenfrom Hevea brasiliensis; At2g26560 5.89 −1.06 0.019374 0.83179 supportedby full-length cDNA: Ceres: 1999. 266800_at hypothetical proteinpredicted by genefinder At2g22880 5.86 −1.01 0.003336 0.993661 259211_atunknown protein identical to GB: AAD56318 At3g09020 5.82 1.08 0.006490.5476 (Arabidopsis thaliana) 253485_at Expressed protein; supported byfull-length cDNA: At4g31800 5.82 −1.13 0.00494 0.428126 Ceres: 40692.260211_at hypothetical protein similar to YGL010w-like At1g74440 5.771.06 0.003351 0.730279 protein GB: AAC32136 [Picea mariana] 256093_atpredicted protein; supported by cDNA: At1g20823 5.74 −1.35 0.0160680.107243 gi_15027984_gb_AY045849.1_(—) 267451_at putative AP2 domaintranscription factor At2g33710 5.72 −1.17 0.015334 0.725714 260411_athypothetical protein similar to GB: AAB61488 At1g69890 5.71 −1.290.011204 0.168552 [Arabidopsis thaliana]; supported by full-length cDNA:Ceres: 34864. 254592_at heat shock transcription factor-like proteinheat At4g18880 5.7 −1.08 0.009829 0.552909 shock transcription factor,Zea mays, PIR2: S61448 264000_at putative mitochondrial dicarboxylatecarrier protein; At2g22500 5.68 −1.18 0.004964 0.182153 supported byfull-length cDNA: Ceres: 20723. 263475_at Expressed protein; supportedby full-length cDNA: At2g31945 5.63 1 0.00655 0.971652 Ceres: 258917.254408_at serine/threonine kinase-like protein serine/threonineAt4g21390 5.63 1.2 0.003477 0.605633 kinase BRLK, Brassica oleracea, gb:Y12531 245209_at putative protein similarity to predicted protein,At5g12340 5.63 −1.23 0.004077 0.532051 Arabidopsis thaliana 259629_atdisease resistance protein contains domains At1g56510 5.61 −1.130.009583 0.608416 associated with disease resistance genes in plants:TIR/NB-ARC/LRR 247655_at zinc finger protein Zat12; supported byfull-length At5g59820 5.56 1.2 0.004335 0.099425 cDNA: Ceres: 40576.266834_s_at putative protein phosphatase 2C At2g30020 5.52 −1.030.005778 0.730603 256181_at light repressible receptor protein kinase,putative At1g51820 5.51 −1.08 0.002365 0.605128 similar to lightrepressible receptor protein kinase GI: 1321686 from (Arabidopsisthaliana) 251705_at DNA-binding protein-like DNA-binding protein 4At3g56400 5.5 −1.03 0.00667 0.83389 WRKY4-Nicotiana tabacum, EMBL:AF193771; supported by full-length cDNA: Ceres: 34847. 251097_atreceptor like protein kinase receptor like protein At5g01560 5.48 −1.090.00945 0.858858 kinase-Arabidopsis thaliana, EMBL: ATLECGENE 248392_atintegral membrane protein-like At5g52050 5.45 −1.21 0.005162 0.477438254158_at putative protein dihydrofolate reductase- At4g24380 5.44 −1.170.013347 0.342417 Schizosaccharomyces pombe, PID: e1320950; supported byfull-length cDNA: Ceres: 27155. 260406_at putative glutathionetransferase similar to glutathione At1g69920 5.41 2.07 0.009635 0.082596transferase GB: CAA09188 [Alopecurus myosuroides] 254241_atserine/threonine kinase-like protein serine/threonine At4g23190 5.371.09 0.001802 0.566443 kinase, Brassica oleracea 265674_at unknownprotein; supported by full-length cDNA: At2g32190 5.3 1.24 0.0133330.440285 Ceres: 40344. 264757_at receptor protein kinase (IRK1),putative similar to At1g61360 5.28 −1.05 0.002166 0.73136 receptorprotein kinase (IRK1) GI: 836953 from [Ipomoea trifida] 248875_atdisease resistance protein-like At5g46470 5.28 −1.01 0.004999 0.943089247708_at putative protein COP1-interacting protein CIP8, At5g59550 5.28−1.21 0.003861 0.156044 Arabidopsis thaliana, EMBL: AF162150; supportedby cDNA: gi_15450686_gb_AY052711.1_(—) 260239_at putative receptorprotein kinase similar to At1g74360 5.26 1.27 0.014165 0.212238brassinosteroid insensitive 1 GB: AAC49810 (putative receptor proteinkinase); contains Pfam profiles: PF00560 Leucine Rich Repeat (17repeats), PF00069 Eukaryotic protein kinase domain; supported by cDNA:gi_158 255549_at predicted protein of unknown function At4g01950 5.23−1.02 0.009729 0.893458 266992_at similar to Mlo proteins from H.vulgare; supported At2g39200 5.21 −1.12 0.008101 0.282992 by cDNA:gi_14091593_gb_AF369573.1_AF369573 261973_at hypothetical proteinpredicted by genemark.hmm At1g64610 5.19 −1.09 0.005786 0.674167254242_at serine/threonine kinase-like protein serine/ At4g23200 5.191.03 0.007882 0.840853 threonine kinase, Brassica oleracea 260477_atSer/Thr protein kinase isolog At1g11050 5.15 −1.34 0.029135 0.243484265670_s_at unknown protein; supported by full-length cDNA: At2g322105.07 1.19 0.014682 0.138268 Ceres: 31665. 265199_s_at putative glucosyltransferase At2g36770 5.07 1.33 0.003771 0.194926 247493_at copine-likeprotein copine I, Homo sapiens, At5g61900 5.07 1.04 0.003077 0.714944EMBL: HSU83246; supported by full-length cDNA: Ceres: 146738. 265737_atputative phosphatidic acid phosphatase; supported At2g01180 5.04 −1.050.00382 0.74519 by full-length cDNA: Ceres: 19163. 260243_athypothetical protein similar to putative protein At1g63720 5.01 1.070.019639 0.772243 GB: CAA18164 [Arabidopsis thaliana]; supported bycDNA: gi_13878144_gb_AF370335.1_AF370335 252045_at putative protein armrepeat containing protein ARC1- At3g52450 5.01 1.25 0.012091 0.125673Brassica napus, PID: g2558938 250153_at putative protein TMVresponse-related gene product, At5g15130 5 1.05 0.011689 0.809857Nicotiana tabacum, EMBL: AB024510 247047_at putative protein containssimilarity to unknown At5g66650 4.98 −1.01 0.006647 0.888192 protein (gbAAC17084.1); supported by cDNA: gi_14596230_gb_AY042903.1_(—) 261476_athypothetical protein contains similarity to alpha- At1g14480 4.97 1.140.02789 0.562278 latroinsectotoxin precursor GI: 9537 from [Latrodectustredecimguttatus] 247205_at unknown protein; supported by full-lengthcDNA: At5g64890 4.96 1.59 0.010532 0.389292 Ceres: 9242. 261450_s_atO-methyltransferase, putative similar to At1g21110 4.95 1.5 0.022030.137219 GB: AAF28353 from [Fragaria × ananassa] 252474_at putativeprotein several hypothetical proteins- At3g46620 4.94 −1.06 0.0066330.705845 Arabidopsis thaliana 257840_at protein kinase, putativecontains Pfam profile: At3g25250 4.93 1.19 0.013824 0.496857 PF00069Eukaryotic protein kinase domain 248964_at cytochrome P450 At5g453404.93 −1.52 0.003815 0.013613 247071_at putative protein similar tounknown protein (emb At5g66640 4.92 −1.02 0.010559 0.987089 CAB16816.1)246270_at putative protein At4g36500 4.92 −1.2 0.002823 0.230335261033_at unknown protein; supported by full-length cDNA: At1g17380 4.84−1.01 0.017643 0.96188 Ceres: 37370. 260261_at unknown protein At1g684504.78 −1.03 0.006946 0.882923 249485_at receptor protein kinase-likeprotein receptor-protein At5g39020 4.74 1.03 0.002268 0.823569kinase-like protein, Arabidopsis thaliana, PIR: T45786 256487_at diseaseresistance gene, putative similar to downy At1g31540 4.73 1.14 0.011070.679977 mildew resistance protein RPP5 [Arabidopsis thaliana] GI:6449046 249983_at putative protein S-receptor kinase PK3 precursor,At5g18470 4.69 1.03 0.006021 0.801393 maize, PIR: T02753; supported byfull-length cDNA: Ceres: 154037. 258682_at putative ribosomal-protein S6kinase (ATPK19) At3g08720 4.68 1.12 0.009464 0.260404 identical toputative ribosomal-protein S6 kinase (ATPK19) GB: D42061 [Arabidopsisthaliana] (FEBS Lett. 358 (2), 199-204 (1995)); supported by cDNA:gi_15292784_gb_AY050826.1_(—) 254487_at calcium-binding protein-likecalcium-binding At4g20780 4.63 −1.43 0.015022 0.176224 protein, Solanumtuberosum, gb: L02830 265728_at hypothetical protein predicted bygenscan At2g31990 4.62 −1.14 0.025876 0.616683 258792_at hypotheticalprotein predicted by At3g04640 4.62 −1.08 0.003809 0.521094 genefinder;supported by full-length cDNA: Ceres: 8992. 253535_at putaiveDNA-binding protein DNA-binding protein At4g31550 4.62 −1.17 0.0016160.072643 WRKY3-Petroselinum crispum, PIR2: S72445; supported byfull-length cDNA: Ceres: 11953. 257751_at hypothetical protein predictedby At3g18690 4.6 −1.01 0.006195 0.939184 genemark.hmm; supported byfull-length cDNA: Ceres: 104278. 261367_at protein kinase, putativesimilar to many predicted At1g53080 4.59 1.31 0.008723 0.439817 proteinkinases 247240_at putative protein strong similarity to unknown proteinAt5g64660 4.57 −1.08 0.004191 0.392312 (emb|CAB89350.1) 261526_atprotein kinase identical to protein kinase GI: 2852447 At1g14370 4.56−1.08 0.004758 0.475696 from [Arabidopsis thaliana]; supported by cDNA:gi_2852446_dbj_D88206.1_D88206 254948_at putative protein variouspredicted proteins, At4g11000 4.55 1.03 0.020674 0.901116 Arabidopsisthaliana 245119_at unknown protein; supported by cDNA: At2g41640 4.54−1.2 0.013528 0.323955 gi_16930450_gb_AF419579.1_AF419579 248319_atunknown protein At5g52710 4.5 −1.19 0.022646 0.498394 245765_athypothetical protein similar to putative disease At1g33600 4.5 −1.010.00753 0.943437 resistance protein GB: AAC14512 GI: 2739389 from[Arabidopsis thaliana] 248821_at protein serine threonine kinase-likeAt5g47070 4.49 1.13 0.005807 0.220356 245272_at hypothetical protein;supported by cDNA: At4g17250 4.49 −1 0.016447 0.969266gi_16323154_gb_AY057681.1_(—) 255595_at putative chitinase similar topeanut type II chitinase, At4g01700 4.48 1.09 0.009232 0.455046 GenBankaccession number X82329, E.C. 3.2.1.14 249918_at putative proteinpredicted protein, Arabidopsis At5g19240 4.48 1.11 0.005605 0.490746thaliana 263565_at unknown protein At2g15390 4.45 −1.28 0.0112980.375612 261713_at protein kinase, putative identical to bHLH proteinAt1g32640 4.43 1.12 0.002007 0.392042 GB: CAA67885 GI: 1465368 from[Arabidopsis thaliana]; supported by cDNA: gi_14335047_gb_AY037203.1_(—)262772_at puative calcium-transporting ATPase similar to At1g13210 4.4−1.06 0.004192 0.641809 gb|AF038007 FIC1 gene from Homo sapiens and is amember of the PF|00122 E1-E2 ATPase family. ESTs gb|T45045 andgb|AA394473 come from this gene 258364_at unknown protein At3g14225 4.4−1.49 0.013195 0.305266 257022_at zinc finger protein, putative similarto Cys2/His2- At3g19580 4.39 −1.04 0.01073 0.818188 type zinc fingerprotein 2 GB: BAA85107 from [Arabidopsis thaliana]; supported by cDNA:gi_15028256_gb_AY046043.1_(—) 252053_at syntaxin-like protein synt4;supported by full-length At3g52400 4.38 1.02 0.002866 0.837782 cDNA:Ceres: 37248. 250695_at lectin-like protein kinase At5g06740 4.38 −1.340.030543 0.436678 246293_at SigA binding protein; supported by cDNA:At3g56710 4.38 −1.01 0.005488 0.98387 gi_14596086_gb_AY042831.1_(—)249032_at putative protein contains similarity to disease At5g44910 4.371.06 0.010921 0.589391 resistance protein 265189_at unknown protein;supported by cDNA: At1g23840 4.34 1.12 0.020118 0.585186gi_14335017_gb_AY037188.1_(—) 265668_at putative alanine acetyltransferase; supported by At2g32020 4.31 1.45 0.006627 0.053107full-length cDNA: Ceres: 21201. 264232_at putative protein kinase PfamHMM hit: Eukaryotic At1g67470 4.3 −1.07 0.003961 0.651045 protein kinasedomain; identical to GB: AAC18787 (Arabidopsis thaliana) 263948_atsimilar to harpin-induced protein hin1 from tobacco; At2g35980 4.28 1.340.007735 0.319605 supported by full-length cDNA: Ceres: 26418. 261748_athypothetical protein predicted by At1g76070 4.27 −1.05 0.034903 0.781675genemark.hmm; supported by full-length cDNA: Ceres: 39494. 252278_atNAC2-like protein NAC2-Arabidopsis thaliana, At3g49530 4.25 −1.010.001287 0.915747 EMBL: AF201456; supported by cDNA:gi_16604578_gb_AY059734.1_(—) 247137_at calcium-dependent proteinkinase; supported by At5g66210 4.23 −1.01 0.004474 0.902625 full-lengthcDNA: Ceres: 18901. 255568_at putative DNA-binding protein; supported byAt4g01250 4.21 −1.2 0.010495 0.218487 cDNA:gi_15028172_gb_AY045909.1_(—) 259479_at Expressed protein; supported byfull-length cDNA: At1g19020 4.2 1.23 0.002707 0.175614 Ceres: 31015.245247_at scarecrow-like 13 (SCL13); supported by cDNA: At4g17230 4.21.06 0.010533 0.625637 gi_16930432_gb_AF419570.1_AF419570 252470_atprotein kinase 6-like protein protein kinase 6- At3g46930 4.19 1.130.012875 0.362838 Glycine max, PIR2: S29851 256050_at leucine zipperprotein, putative similar to leucine At1g07000 4.16 1.04 0.0182980.855313 zipper protein GI: 10177020 from [Arabidopsis thaliana]261405_at unknown protein; supported by full-length cDNA: At1g18740 4.15−1.11 0.00951 0.382476 Ceres: 40753. 267288_at similar to coldacclimation protein WCOR413 At2g23680 4.12 1.06 0.026303 0.758149[Triticum aestivum] 252592_at mitogen-activated protein kinase 3;supported by At3g45640 4.12 −1.15 0.004807 0.119458 cDNA:gi_14423447_gb_AF386961.1_AF386961 247125_at putative protein containssimilarity to unknown At5g66070 4.11 1 0.001239 0.979764 protein(gb|AAF18680.1) 265184_at unknown protein; supported by full-lengthcDNA: At1g23710 4.09 −1.18 0.014497 0.24269 Ceres: 36437. 247773_atputative protein At5g58630 4.09 −1.08 0.006176 0.825067 263478_atputative receptor-like protein kinase; supported by At2g31880 4.08 1.140.00624 0.158364 cDNA: gi_16648754_gb_AY058153.1_(—) 251910_atserine/threonine-specific kinase like protein At3g53810 4.05 −1.020.002869 0.843094 serine/threonine-specific kinase (EC 2.7.1.—)precursor-Arabidopsis thaliana, PIR: S68589 245662_at hypotheticalprotein predicted by genemark.hmm At1g28190 4.04 −1.23 0.0328 0.44426259997_at unknown protein similar to N- At1g67880 4.03 1 0.0057670.973619 acetylglucosaminyltransferase III GB: AAC53064 [Mus musculus]252179_at putative protein UDP-glucose: (glucosyl) LPS At3g50760 4.03−1.04 0.00304 0.802486 alpha1,3-glucosyltransferase WaaO, E. coli, EMBL:AF019746 252928_at putative protein more than 30 predicted proteins,At4g38940 4.01 1.07 0.000729 0.325455 Arabidopsis; supported byfull-length cDNA: Ceres: 40069. 251832_at putative protein tomatoleucine zipper-containing At3g55150 4.01 1.41 0.010257 0.134388 protein,Lycopersicon esculentum, PIR: S21495 266396_at unknown protein At2g387904 1.05 0.027395 0.850892 259400_at receptor-like protein kinase,putative similar to At1g17750 3.97 −1.02 0.042252 0.932069 receptor-likeprotein kinase INRPK1 GI: 1684913 from [Ipomoea nil] 255654_at Similarto receptor kinase At4g00970 3.97 −1.11 0.010838 0.737951 254587_atresistance protein RPP5-like downy mildew At4g19520 3.97 −1.05 0.007680.89806 resistance protein RPP5, Arabidopsis thaliana, PATX: G2109275255753_at myb factor, putative similar to myb factor At1g18570 3.95 1.030.004424 0.830522 GI: 1946266 from [Oryza sativa]; supported by cDNA:gi_3941465_gb_AF062887.1_AF062887 246532_at putative proteinbeta-glucan-elicitor receptor- At5g15870 3.94 −1.02 0.015841 0.913394Glycine max, EMBL: D78510 246631_at unknown protein; supported byfull-length cDNA: At1g50740 3.93 1.04 0.006841 0.56351 Ceres: 34587.252533_at putative protein predicted proteins, Arabidopsis At3g46110 3.91.02 0.017185 0.893955 thaliana 267384_at unknown protein highly similarto At2g44370 3.88 1.08 0.005016 0.736235 GP|2435515|AF024504 258650_atputative protein kinase similar to protein kinase At3g09830 3.88 1.110.012936 0.571912 (APK1A) GB: Q06548 [Arabidopsis thaliana]; containsPfam profile: PF00069 Eukaryotic protein kinase domain 249339_atputative protein similar to unknown protein At5g41100 3.88 −1.050.004061 0.72083 (gb|AAB80666.1) 248794_at ethylene responsive elementbinding factor 2 At5g47220 3.87 −1.23 0.011156 0.098663 (ATERF2)(sp|O80338); supported by full-length cDNA: Ceres: 3012. 245457_s_atdisease resistance RPP5 like protein At4g16960 3.86 1.18 0.0102590.375561 248316_at putative protein similar to unknown protein At5g526703.84 −1.03 0.006334 0.875191 (emb|CAA71173.1) 253046_at cytochromeP450-like protein cytochrome P450, At4g37370 3.83 2.17 0.019261 0.016853Glycyrrhiza echinata, AB001379; supported by full- length cDNA: Ceres:253698. 262374_s_at flax rust resistance protein, putative similar toflax At1g72930 3.81 1.03 0.004406 0.567071 rust resistance protein GI:4588066 from [Linumusitatissimum]; supported by full-length cDNA: Ceres:2795. 258537_at putative disease resistance protein similar to diseaseAt3g04210 3.81 1.09 0.005941 0.472196 resistance protein RPP1-WsC GB:AAC72979 [Arabidopsis thaliana]; supported by cDNA:gi_15982829_gb_AY057522.1_(—) 252648_at disease resistance proteinhomolog disease At3g44630 3.81 −1.23 0.007177 0.068548 resistanceprotein RPP1-WsB-Arabidopsis thaliana, EMBL: AF098963 247913_at unknownprotein At5g57510 3.81 1.12 0.009476 0.608703 267411_at putative diseaseresistance protein At2g34930 3.8 −1.06 0.015151 0.825604 265440_atpEARLI 4 protein Same as GB: L43081; supported At2g20960 3.8 −1.080.001968 0.382136 by cDNA: gi_871781_gb_L43081.1_ATHPEARA 245252_atethylene responsive element binding factor 1 At4g17500 3.8 −1.470.008058 0.087956 (frameshift !); supported by cDNA:gi_3434966_dbj_AB008103.1_AB008103 259033_at putativepectinacetylesterase similar to At3g09410 3.79 1.64 0.003796 0.052828pectinacetylesterase precursor GB: CAA67728 [Vigna radiata] 246233_atputative protein At4g36550 3.79 −1.43 0.028755 0.228285 255599_at cyclicnucleotide gated channel (CNGC4) like At4g01010 3.78 −1.02 0.006060.91649 protein Arabidopsis thaliana cyclic nucleotide gated channel(CNGC4), PID: g4378659 262901_at hypothetical protein predicted bygenemark.hmm At1g59910 3.77 −1.08 0.006294 0.540378 259952_at putativedisease resistance protein similar to Cf-4 At1g71400 3.74 1.08 0.0013930.408545 GB: CAA05268 from (Lycopersicon hirsutum) 246858_atreceptor-like protein kinase-like receptor-like At5g25930 3.73 1.020.015786 0.964753 protein kinase 5, Arabidopsis thaliana, PIR: S27756250435_at putative protein various predicted proteins, At5g10380 3.721.22 0.007856 0.106321 Arabidopsis thaliana 261650_at envelopeCa2+-ATPase identical to envelope Ca2+- At1g27770 3.71 1.05 0.008390.580228 ATPase GB: AAD10212 GI: 516118 from (Arabidopsis thaliana);supported by cDNA: gi_493621_dbj_D13983.1_ATHRCECAA 252906_at putativegamma-glutamyltransferase gamma- At4g39640 3.71 1.07 0.012355 0.562612glutamyltransferase, Arabidopsis thaliana, PIR2: S58286 251636_atcalcium-dependent protein kinase calcium- At3g57530 3.71 −1.26 0.0167220.11982 dependent protein kinase-Fragaria × ananassa, EMBL: AF035944247426_at putative protein contains similarity to calmodulin- At5g625703.67 1.02 0.018802 0.878551 binding protein 266685_at hypotheticalprotein At2g19710 3.66 −1 0.018487 0.952139 249903_at disease resistanceprotein-like At5g22690 3.65 −1.04 0.010635 0.754135 247925_at TCH4protein (gb|AAA92363.1); supported by At5g57560 3.65 −1.28 0.0030030.132214 cDNA: gi_14194112_gb_AF367262.1_AF367262 248611_at putativeprotein contains similarity to WRKY-type At5g49520 3.63 −1.45 0.0109660.13904 DNA-binding protein 265221_s_at putative glutamatedecarboxylase; supported by At2g02010 3.62 −1.12 0.01727 0.698419 cDNA:gi_13605709_gb_AF361836.1_AF361836 259792_at unknown protein; supportedby cDNA: At1g29690 3.62 −1.05 0.013953 0.685925gi_15809819_gb_AY054177.1_(—) 256576_at zinc finger protein (PMZ),putative identical to At3g28210 3.62 1.34 0.019514 0.107277 putativezinc finger protein (PMZ) GB: AAD37511 GI: 5006473 [Arabidopsisthaliana] 254784_at growth factor like protein antisense basicfibroblast At4g12720 3.62 1.06 0.012904 0.638871 growth factorGFG-Rattus norvegicus, PID: g1518635; supported by full-length cDNA:Ceres: 148575. 247177_at unknown protein; supported by cDNA: At5g653003.62 1.1 0.004863 0.387978 gi_13877834_gb_AF370180.1_AF370180 245226_atgene_id: K17E7.15~unknown protein At3g29970 3.6 1.76 0.01017 0.066452256756_at ATPase II, putative similar to GB: AAD34706 from At3g256103.59 −1.01 0.009255 0.929097 [Homo sapiens] (Biochem. Biophys. Res.Commun. 257 (2), 333-339 (1999)) 253140_at RING-H2 finger protein RHA3b;supported by full- At4g35480 3.56 −1.04 0.013391 0.651703 length cDNA:Ceres: 31493. 250289_at putative protein; supported by full-length cDNA:At5g13190 3.56 1.18 0.000966 0.176346 Ceres: 5392. 247811_at leucinezipper-containing protein leucine zipper- At5g58430 3.56 −1.01 0.0013440.933016 containing protein, Lycopersicon esculentum, PIR: S21495261899_at cinnamoyl CoA reductase, putative similar to At1g80820 3.55−1.11 0.01598 0.720481 cinnamoyl CoA reductase GB: AAF43141 GI: 7239228from [Populus tremuloides]; supported by full-length cDNA: Ceres: 32255.245866_s_at unknown protein At1g57990 3.55 −1.09 0.011056 0.501011264867_at unknown protein At1g24150 3.53 −1 0.030643 0.978236 261193_atunknown protein; supported by cDNA: At1g32920 3.53 −1.12 0.0094890.382199 gi_15450636_gb_AY052686.1_(—) 261339_at protein kinase,putative similar to many predicted At1g35710 3.51 1.32 0.013195 0.062019protein kinases 267490_at putative receptor-like protein kinaseAt2g19130 3.5 1 0.015702 0.997521 259561_at hypothetical protein;supported by cDNA: At1g21250 3.49 1.52 0.005151 0.042781gi_14532585_gb_AY039917.1_(—) 263228_at putative reticuline oxidase-likeprotein similar to At1g30700 3.48 1.07 0.007823 0.648304 GB: P30986 from[Eschscholzia californica] (berberine bridge-forming enzyme), ESTsgb|F19886, gb|Z30784 and gb|Z30785 come from this gene; supported bycDNA: gi_16930506_gb_AF419607.1_AF419607 255627_at Expressed protein;supported by full-length cDNA: At4g00955 3.48 1.08 0.009206 0.72176Ceres: 93818. 254256_at serine/threonine kinase-like proteinserine/threonine At4g23180 3.45 −1.2 0.002919 0.140829 kinase, Brassicaoleracea; supported by cDNA: gi_13506744_gb_AF224705.1_AF224705260135_at calmodulin-related protein similar to GB: P25070 At1g664003.44 −1.11 0.013883 0.371779 from [Arabidopsis thaliana], contains Pfamprofile: PF00036 EF hand (4 copies); supported by full- length cDNA:Ceres: 95959. 260206_at putative protein kinase contains Pfam profile:At1g70740 3.43 −1.12 0.012329 0.420329 PF00069 Eukaryotic protein kinasedomain 259887_at putative protein kinase similar to protein kinaseAt1g76360 3.42 1.1 0.008975 0.501823 (APK1A); contains Pfam profile:PF00069 Eukaryotic protein kinase domain 262383_at disease resistanceprotein, putative similar to disease At1g72940 3.41 1.18 0.0119420.230832 resistance protein GI: 9758876 from [Arabidopsis thaliana]256177_at protein kinase, putative contains Pfam profile: At1g51620 3.411.23 0.01444 0.359679 PF00069: Eukaryotic protein kinase domain245777_at unknown protein contains similarity to At1g73540 3.41 −1.250.026487 0.341823 diphosphoinositol polyphosphate phosphohydrolase GI:3978224 from [Homo sapiens] 249221_at serine/threonine proteinkinase-like protein At5g42440 3.4 −1.02 0.005295 0.883947 245448_atdisease resistance RPP5 like protein At4g16860 3.4 −1.15 0.0279850.375642 254869_at protein kinase-like protein KI domain interactingAt4g11890 3.37 2.12 0.007665 0.003284 kinase 1-Zea mays, PIR2: T02053256755_at calmodulin, putative similar to GB: P07463 from At3g25600 3.37−1.05 0.007284 0.663209 [Paramecium tetraurelia] (Cell 62 (1), 165-174(1990)) 264107_s_at putative receptor-like protein kinase At2g13790 3.341.16 0.008131 0.293891 266017_at unknown protein; supported by cDNA:At2g18690 3.32 1.36 0.008527 0.108178 gi_14517479_gb_AY039575.1_(—)263776_s_at putative cyclic nucleotide-regulated ion channel At2g464403.32 1.21 0.026465 0.278033 protein 245193_at F12A21.6 hypotheticalprotein At1g67810 3.32 1.17 0.00613 0.205789 256522_at unknown protein;supported by full-length cDNA: At1g66160 3.3 −1.22 0.004073 0.074994Ceres: 35218. 248703_at dermal glycoprotein precursor,extracellular-like At5g48430 3.28 1.09 0.005001 0.574329 260434_athypothetical protein predicted by genscan+ At1g68330 3.27 −1.14 0.0061280.614427 252652_at putative chloroplast prephenate dehydratase similarAt3g44720 3.23 1.08 0.004759 0.192206 to bacterial PheA gene products260023_at unknown protein At1g30040 3.21 1.26 0.004354 0.301041251640_at putative protein; supported by full-length cDNA: At3g574503.21 −1.03 0.002724 0.717428 Ceres: 12522. 264314_at unknown protein;supported by cDNA: At1g70420 3.18 1.24 0.00926 0.33473gi_15010575_gb_AY045589.1_(—) 262549_at hypothetical protein similar tohypothetical protein At1g31290 3.18 1.36 0.017342 0.141779 GB: AAF24586GI: 6692121 from [Arabidopsis thaliana] 261459_at O-methyltransferase,putative similar to At1g21100 3.18 1.37 0.006504 0.199125 GB: AAF28353from [Fragaria × ananassa]; supported by cDNA:gi_15982843_gb_AY057529.1_(—) 249139_at Cys2/His2-type zinc fingerprotein 3 At5g43170 3.18 −1.11 0.014619 0.403291 (dbj|BAA85109.1);supported by full-length cDNA: Ceres: 9878. 248980_at putative proteinsimilar to unknown protein At5g45090 3.18 −1.03 0.006572 0.837241(pir||T04765) 264660_at putative glutamyl-tRNA reductase 2 precursorAt1g09940 3.17 −1.02 0.009351 0.857849 similar to GB: P49294 and to A.thaliana HEMA2 (gb|U27118) 254014_at NPR1 like protein regulatoryprotein NPR1- At4g26120 3.17 1.03 0.021113 0.898299 Arabidopsisthaliana, PID: g1773295 252126_at putative disease resistance proteinAt3g50950 3.17 1.08 0.00517 0.256863 262228_at protein kinase, putativesimilar to protein kinase 1 At1g68690 3.16 1.18 0.018754 0.421396 GB:BAA94509 GI: 7573596 from [Populus nigra]; supported by cDNA:gi_14334805_gb_AY035076.1_(—) 259626_at bZIP transcription factor,putative contains Pfam At1g42990 3.15 1.08 0.006031 0.361959 profile:PF00170: bZIP transcription factor; supported by cDNA:gi_15028322_gb_AY045964.1_(—) 254063_at receptor kinase-like proteinreceptor-like protein At4g25390 3.15 −1.09 0.021274 0.509081 kinase,RLK3-Arabidopsis thaliana, PID: e1363211 259443_at chitinase, putativesimilar to chitinase GI: 1237025 At1g02360 3.14 1.33 0.010757 0.097826from [Arachis hypogaea] 266615_s_at putative monooxygenase; supported byfull-length At2g29720 3.13 −1 0.006073 0.993995 cDNA: Ceres: 34214.251507_at putative protein CND41, chloroplast nucleoid DNA At3g590803.13 −1.26 0.019246 0.076416 binding protein-Nicotiana tabacum, EMBL:D26015; supported by cDNA: gi_15983375_gb_AF424562.1_AF424562 246870_atferrochelatase-I At5g26030 3.12 −1.03 0.007971 0.563075 261063_attranscription factor scarecrow-like 14, putative At1g07520 3.09 1.050.0041 0.648222 similar to GB: AAD24412 from [Arabidopsis thaliana](Plant J. 18 (1), 111-119 (1999)) 260296_at putative disease resistanceprotein similar to disease At1g63750 3.07 −1.24 0.035995 0.346342resistance protein (RPP1-WsC) GB: AAC72979 [Arabidopsis thaliana]248868_at putative protein similar to unknown protein At5g46780 3.071.08 0.012841 0.668687 (gb|AAC61815.1); supported by full-length cDNA:Ceres: 254442. 267069_at unknown protein At2g41010 3.06 −1 0.0229320.942266 261143_at unknown protein At1g19770 3.06 −1.07 0.0030120.469481 255116_at receptor protein kinase-like protein receptor proteinAt4g08850 3.06 1.13 0.013035 0.33618 kinase-like protein-Arabidopsisthaliana, PIR2: T05898 253284_at putative protein hydroxyproline-richglycoprotein At4g34150 3.05 1.01 0.004615 0.829133 precursor, Nicotianatabacum, PIR2: S06733; supported by cDNA:gi_15724315_gb_AF412098.1_AF412098 252903_at putative protein variouspredicted proteins, At4g39570 3.05 −1.05 0.005467 0.697229 Arabidopsisthaliana 254847_at putative phospholipase D-gamma phospholipase D-At4g11850 3.04 −1.01 0.014523 0.911568 gamma-Arabidopsis thaliana, PID:g2653885; supported by cDNA: gi_2653884_gb_AF027408.1_AF027408 251937_atputative protein predicted protein, Arabidopsis At3g53400 3.04 1.040.035806 0.858509 thaliana 256366_at protein kinase, putative containsPfam profile: At1g66880 3.03 1.12 0.002701 0.411044 PF00069: Eukaryoticprotein kinase domain 247393_at unknown protein At5g63130 3.03 −1.650.018398 0.063566 260556_at putative endochitinase At2g43620 3.02 1.320.003455 0.0287 259445_at dioxygenase, putative similar to dioxygenaseAt1g02400 3.01 1.16 0.012122 0.130623 GI: 1666096 from [Marahmacrocarpus] 259298_at putative disease resistance protein similar toCf-2 At3g05370 3.01 −1.08 0.040444 0.621247 disease resistance proteinGB: AAC15780 from [Lycopersicon pimpinellifolium] 257644_at unknownprotein; supported by full-length cDNA: At3g25780 3.01 1.19 0.0227720.336306 Ceres: 3457. 253628_at xyloglucanendo-1,4-beta-D-glucanase-like protein At4g30280 3.01 1.29 0.0058420.110446 xyloglucan endo-1,4-beta-D-glucanase (EC 3.2.1.—)XTR-3-Arabidopsis thaliana, PIR2: S71222; supported by full-length cDNA:Ceres: 142204. 249072_at putative protein similar to unknown proteinAt5g44060 3.01 1.08 0.007698 0.56653 (gb|AAD10670.1) 253257_atextra-large G-protein-like extra-large G-protein, At4g34390 3 −1.060.004333 0.352585 Arabidopsis thaliana, AF060942 253124_at putativeprotein unknown protein Arabidopsis At4g36030 3 −1.07 0.016993 0.706449thaliana, PATX: E248475 250676_at harpin-induced protein-like; supportedby cDNA: At5g06320 3 1.02 0.003772 0.798472gi_9502175_gb_AF264699.1_AF264699 266037_at putative protein kinasecontains a protein kinase At2g05940 2.99 1.03 0.011895 0.742301 domainprofile (PDOC00100); supported by cDNA: gi_15810412_gb_AY056245.1_(—)254314_at extensin-like protein hybrid proline-rich protein, At4g224702.98 −1.04 0.013677 0.797081 Zea mays, PIR2: JQ1663 252825_at smallGTP-binding protein-like SR1 Nt-rab6, At4g39890 2.97 1.25 0.0142690.471148 Nicotiana tabacum, L29273; supported by cDNA:gi_14423429_gb_AF386952.1_AF386952 260401_at unknown protein similar tohypothetical protein At1g69840 2.96 1.19 0.013016 0.197702 GB: CAA10289[Cicer arietinum] 250821_at putative protein similar to unknown proteinAt5g05190 2.95 −1.11 0.008801 0.532383 (emb|CAB88044.1) 245265_athypothetical protein; supported by cDNA: At4g14400 2.95 1.34 0.0467740.092249 gi_15810232_gb_AY056155.1_(—) 264289_at hypothetical proteinsimilar to hypothetical protein At1g61890 2.94 1.17 0.016735 0.217477GI: 2894569 from [Arabidopsis thaliana]; supported by cDNA:gi_15028186_gb_AY045916.1_(—) 259410_at hypothetical protein predictedby genemark.hmm At1g13340 2.94 1.45 0.015002 0.097363 253958_at putativeprotein RING zinc finger protein, Gallus At4g26400 2.94 1.06 0.0026190.621194 gallus 249078_at phytochelatin synthase (gb|AAD41794.1);At5g44070 2.94 −1.02 0.008033 0.806261 supported by cDNA:gi_14532653_gb_AY039951.1_(—) 267293_at hypothetical protein At2g238102.93 −1.06 0.004637 0.578539 259992_at putative heat shock transcriptionfactor contains At1g67970 2.93 −1.01 0.006051 0.910383 Pfam profile:PF00447 HSF-type DNA-binding domain; N-terminal portion similar to heatshock transcription factor proteins: GB: CAA74397 [Arabidopsisthaliana], GB: S25478 [Lycopersicon esculentum] 252862_at putativeL-ascorbate oxidase L-ascorbate oxidase, At4g39830 2.93 1.13 0.0097560.383415 Cucumis sativus, PIR1: KSKVAO 249550_at protein kinase-likeprotein wall-associated kinase 4 At5g38210 2.93 −1.13 0.00676 0.38925(wak4), Arabidopsis thaliana, EMBL: ATH9695 247279_atarabinogalactan-protein (gb|AAC77823.1); At5g64310 2.93 −1.01 0.006610.937671 supported by full-length cDNA: Ceres: 25423. 265450_athypothetical protein predicted by genefinder At2g46620 2.92 −1.030.014924 0.733991 251479_at serine/threonine-specific kinase lecRK1At3g59700 2.91 −1.08 0.008769 0.515335 precursor, lectin receptor-like249418_at putative protein predicted protein, Arabidopsis At5g39780 2.911.1 0.015458 0.521455 thaliana 266247_at hypothetical protein predictedby genscan At2g27660 2.89 −1.11 0.009688 0.350456 249252_at putativeprotein contains similarity to unknown At5g42010 2.89 −1.05 0.0140730.747236 protein (gb|AAF19687.1) 255291_at putative calcium dependentprotein kinase At4g04700 2.88 −1.04 0.023496 0.890022 253747_at serinethreonine-specific kinase like protein serine At4g29050 2.87 −1.090.011457 0.626019 threonine-specific kinase lecRK1-Arabidopsis thaliana,PIR2: S68589 250323_at putative protein hydroxyproline-richglycoprotein, At5g12880 2.87 1.06 0.009216 0.469664 kidney bean, PIR:A29356 262801_at unknown protein; supported by full-length cDNA:At1g21010 2.86 1.08 0.017653 0.443505 Ceres: 17521. 251061_at putativeprotein hypothetical protein ARC1- At5g01830 2.86 1.18 0.015743 0.623238Brassica napus, PIR: T08872 265132_at unknown protein; supported bycDNA: At1g23830 2.84 −1.07 0.017467 0.652241gi_16604403_gb_AY058100.1_(—) 260439_at hypothetical protein predictedby At1g68340 2.84 −1.04 0.003917 0.840841 genscan+; supported byfull-length cDNA: Ceres: 3385. 260227_at unknown protein similar tohypothetical proteins At1g74450 2.83 −1.16 0.009649 0.269848 GB:AAD39276 [Arabidopsis thaliana], GB: CAB53491 [Oryza sativa]; supportedby full- length cDNA: Ceres: 108193. 261453_at O-methyltransferase,putative similar to At1g21130 2.82 −1.15 0.010888 0.513201 GB: AAF28353from [Fragaria × ananassa]; supported by full-length cDNA: Ceres:101583. 254432_at reticuline oxidase-like protein reticuline oxidase,At4g20830 2.82 1.19 0.046062 0.572211 Eschscholzia californica, PIR:A41533; supported by cDNA: gi_15983492_gb_AF424621.1_AF424621 253971_atfructose-bisphosphate aldolase-like protein At4g26530 2.82 −1.020.016712 0.805977 fructose-bisphosphate aldolase, Arabidopsis thaliana,PIR1: ADMU; supported by full-length cDNA: Ceres: 34690. 262165_atputative acyl-CoA: 1-acylglycerol-3-phosphate At1g75020 2.81 −1.130.010295 0.275107 acyltransferase similar to acyl-CoA: 1-acylglycerol-3-phosphate acyltransferase GB: CAB09138 (Brassica napus); contains Pfamprofile: PF01553 Acyltransferase; supported by full-length cDNA: Ceres:115679. 258275_at unknown protein; supported by full-length cDNA:At3g15760 2.81 −1.09 0.002884 0.259472 Ceres: 8259. 255564_s_athypothetical protein T15B16.8 At4g01750 2.81 1.28 0.004474 0.364426253377_at putative protein NBS/LRR disease resistance protein At4g333002.81 1.03 0.008788 0.64371 (RFL1)-Arabidopsis thaliana, PID: g3309619260220_at putative MYB family transcription factor contains At1g746502.8 −1.05 0.014801 0.787419 Pfam profile: PF00249 Myb-like DNA-bindingdomain 256583_at hypothetical protein At3g28850 2.8 1.08 0.0098720.39554 252193_at R2R3-MYB transcription factor; supported by At3g500602.8 −1.67 0.007202 0.02821 cDNA: gi_15983427_gb_AF424588.1_AF424588247509_at heat shock factor 6 At5g62020 2.8 1.11 0.004718 0.497285246368_at light repressible receptor protein kinase, putative At1g518902.8 1.32 0.007014 0.17566 similar to light repressible receptor proteinkinase GI: 1321686 from [Arabidopsis thaliana] 259507_at unknown proteinAt1g43910 2.79 1.41 0.005884 0.156323 251769_at receptor kinase-likeprotein receptor kinase At3g55950 2.79 1.02 0.037029 0.858886 homologCRINKLY4, maize, PIR: T04108 250335_at lysophospholipase-like proteinlysophospholipase At5g11650 2.78 1.07 0.004853 0.539031 homolog LPL1,Oryza sativa, EMBL: AF039531; supported by full-length cDNA: Ceres:15284. 248134_at putative protein contains similarity to integralAt5g54860 2.78 1.09 0.010767 0.465367 membrane protein 246988_atputative protein strong similarity to unknown protein At5g67340 2.781.18 0.01807 0.609865 (pir||T00518) 247707_at scarecrow-like 11-likescarecrow-like 11, At5g59450 2.76 −1.06 0.028093 0.649019 Arabidopsisthaliana, EMBL: AF036307; supported by cDNA:gi_14334655_gb_AY035001.1_(—) 256497_at ORF1, putative similar to ORF1GI: 457716 from At1g31580 2.75 1.39 0.004888 0.080053 (Arabidopsisthaliana); supported by cDNA: gi_16649160_gb_AY059950.1_(—) 264008_atunknown protein At2g21120 2.74 −1.01 0.003042 0.876414 264716_at matrixmetalloproteinase, putative similar to matrix At1g70170 2.73 −1.020.005524 0.873758 metalloproteinase GI: 7159629 from [Cucumis sativus]261445_at unknown protein; supported by cDNA: At1g28380 2.73 −1.060.02128 0.701956 gi_16604598_gb_AY059744.1_(—) 256968_at unknown proteinAt3g21070 2.73 −1.14 0.014315 0.494381 256763_at unknown proteinAt3g16860 2.73 −1.06 0.01099 0.724699 255605_at hypothetical proteinAt4g01090 2.73 −1.18 0.02941 0.263496 254652_at DNA binding-like proteinSPF1 protein, sweet At4g18170 2.73 1.05 0.048645 0.839297 protein, PIR2:S51529 and WRKY protein family, Petroselinum crispum, MNOS: S72443,MNOS: S72444, MNOS: S72445 247532_at putative protein disease resistanceprotein kinase Pto, At5g61560 2.73 −1.03 0.020053 0.845513 Lycopersioconesculentum, PIR: A49332 264106_at unknown protein At2g13780 2.71 1.20.013998 0.074305 265075_at hypothetical protein similar toembryo-abundant At1g55450 2.7 −1.08 0.016743 0.546091 protein GB: L47672GI: 1350530 from [Picea glauca]; supported by cDNA:gi_14335021_gb_AY037190.1_(—) 256793_at unknown protein; supported byfull-length cDNA: At3g22160 2.69 −1.09 0.013465 0.391312 Ceres: 8081.258551_at hypothetical protein predicted by At3g06890 2.68 −1.020.016594 0.966946 genscan+; supported by full-length cDNA: Ceres:262487. 255740_at wall-associated kinase, putative similar to wall-At1g25390 2.68 −1.15 0.012139 0.281008 associated kinase 1 GI: 3549626from [Arabidopsis thaliana]; supported by cDNA:gi_15529241_gb_AY052245.1_(—) 246099_at blue copper binding protein;supported by full- At5g20230 2.67 1.7 0.008061 0.011289 length cDNA:Ceres: 7767. 264616_at unknown protein At2g17740 2.67 1 0.0229170.884668 254042_at xyloglucan endo-1,4-beta-D-glucanase (XTR-6);At4g25810 2.66 1.07 0.002288 0.480301 supported by cDNA:gi_1244757_gb_U43488.1_ATU43488 246289_at putative protein predictedprotein At2g41010- At3g56880 2.66 −1.02 0.010884 0.82618 Arabidopsisthaliana; EMBL: AC004261; supported by full-length cDNA: Ceres: 39584.266792_at putative sucrose/H+ symporter At2g02860 2.65 1.05 0.0051940.618209 265853_at putative RING zinc finger protein At2g42360 2.64 1.270.007875 0.101121 258786_at putative syntaxin contains Pfam profile:PF00804 At3g11820 2.64 1.16 0.005501 0.095192 syntaxin; supported byfull-length cDNA: Ceres: 38899. 247940_at phosphatidylserinedecarboxylase At5g57190 2.64 −1.08 0.02156 0.742477 257083_s_at non-racespecific disease resistance protein, putative At3g20590 2.63 −1.10.022335 0.571353 contains non-consensus CT donor splice site at exon 1;potential pseudogene; similar to non-race specific disease resistanceprotein GB: AAB95208 [Arabidopsis thaliana] 264434_at hypotheticalprotein predicted by genscan; supported At1g10340 2.61 1.14 0.0165380.421888 by cDNA: gi_13937239_gb_AF372975.1_AF372975 263804_at putativeprotein kinase contains a protein kinase At2g40270 2.61 1.02 0.0028010.766513 domain profile (PDOC00100); supported by full- length cDNA:Ceres: 123911. 249896_at unknown protein; supported by cDNA: At5g225302.61 1.12 0.01975 0.439704 gi_14532613_gb_AY039931.1_(—) 249459_atperoxidase ATP24a At5g39580 2.61 −1.24 0.011537 0.098646 247740_atreceptor-like protein kinase precursor-like receptor- At5g58940 2.611.11 0.013363 0.45095 like protein kinase precursor, Madagascarperiwinkle, PIR: T10060 246931_at putative protein apoptosis-relatedprotein PNAS-4, At5g25170 2.6 1.01 0.003003 0.89146 Homo sapiens, EMBL:AF229834; supported by full- length cDNA: Ceres: 263500. 265713_atputative integral membrane protein At2g03530 2.59 −1.18 0.0102840.275593 263931_at unknown protein; supported by full-length cDNA:At2g36220 2.59 1.04 0.032332 0.640228 Ceres: 12251. 264834_at unknownprotein similar to ESTs gb|AA605440 and At1g03730 2.58 1.02 0.0060420.863016 gb|H37232; supported by full-length cDNA: Ceres: 30716.259852_at disulfide bond formation protein, putative similar toAt1g72280 2.58 1.24 0.014598 0.356183 GI: 6642925 from [Mus musculus]252539_at putative protein At3g45730 2.58 1.3 0.009508 0.150314252378_at receptor kinase-like protein protein kinase Xa21- At3g475702.58 1.12 0.02363 0.435178 Oryza sativa, PIR: A57676; supported by cDNA:gi_15810450_gb_AY056264.1_(—) 251684_at putative protein At3g56410 2.571.08 0.023561 0.592162 261719_at hypothetical protein similar tohypothetical protein At1g18380 2.56 1.36 0.016331 0.094821 GB: AAF25996GI: 6714300 from [Arabidopsis thaliana] 254248_at serine/threoninekinase serine/threonine kinase, At4g23270 2.56 −1.04 0.006144 0.687459Brassica oleracea 253204_at GTP binding protein beta subunit; supportedby At4g34460 2.56 −1.01 0.007411 0.949586 cDNA:gi_15028006_gb_AY045860.1_(—) 249361_at protein kinase-like proteinprotein kinase ATN1, At5g40540 2.55 −1 0.004647 0.984046 Arabidopsisthaliana, PIR: S61766 248665_at Expressed protein; supported byfull-length cDNA: At5g48655 2.55 1.02 0.009359 0.848153 Ceres: 12974.253455_at putative protein At4g32020 2.54 −1.01 0.00825 0.888496248978_at putative protein contains similarity to disease At5g45070 2.54−1.05 0.030143 0.671649 resistance protein 248870_at putative proteinsimilar to unknown protein At5g46710 2.54 1.03 0.004547 0.48662(pir||T05076); supported by full-length cDNA: Ceres: 42747. 252170_athypothetical protein; supported by cDNA: At3g50480 2.53 1.09 0.006470.431092 gi_13605735_gb_AF361849.1_AF361849 264636_at hypotheticalprotein predicted by At1g65490 2.52 1.04 0.019945 0.653146 genemark.hmm;supported by full-length cDNA: Ceres: 2118. 264400_atglucose-6-phosphate/phosphate-translocator At1g61800 2.51 −1.13 0.0358530.380949 precursor, putative similar to glucose-6-phosphate/phosphate-translocator precursor GI: 2997591 from [Pisumsativum]; supported by cDNA: gi_14596172_gb_AY042874.1_(—) 245567_atgermin precursor oxalate oxidase At4g14630 2.51 −1.12 0.010395 0.322763264083_at ethylene reponse factor-like AP2 domain At2g31230 2.5 −1.090.007348 0.596007 transcription factor 261220_at ER lumenprotein-retaining receptor similar to At1g19970 2.5 1.11 0.012470.321046 SP: O44017 from [Entamoeba histolytica] 259546_at unknownprotein At1g35350 2.49 −1.02 0.009622 0.86289 266101_at unknown protein;supported by cDNA: At2g37940 2.47 1.05 0.006689 0.366431gi_16604321_gb_AY058059.1_(—) 262384_at disease resistance protein,putative similar to disease At1g72950 2.47 −1.07 0.017043 0.63375resistance protein GI: 9758876 from [Arabidopsis thaliana] 251423_atregulatory protein-like regulatory protein preg, At3g60550 2.47 1.040.005454 0.86361 Neurospora crassa, PIR: S52974 259312_at putativeRING-H2 zinc finger protein ATL6 similar At3g05200 2.46 −1.11 0.0205430.252889 to GB: AAD33584 from [Arabidopsis thaliana]; supported by cDNA:gi_4928402_gb_AF132016.1_AF132016 267624_at putative protein kinaseAt2g39660 2.45 −1.1 0.015362 0.313576 266230_at hypothetical proteinpredicted by genscan and At2g28830 2.45 1.03 0.03586 0.739871genefinder; supported by cDNA: gi_14334729_gb_AY035038.1_(—) 260656_athypothetical protein predicted by genemark.hmm At1g19380 2.45 1.120.012154 0.152235 253664_at NADPH-ferrihemoprotein reductase (ATR2)At4g30210 2.45 1.06 0.014893 0.463357 251259_at putative proteinphosphoprotein phosphatase (EC At3g62260 2.45 1.09 0.008555 0.4955613.1.3.16) 1A-alpha-Homo sapiens, PIR: S22423; supported by full-lengthcDNA: Ceres: 20050. 267357_at putative nematode-resistance protein;supported by At2g40000 2.44 1.16 0.031618 0.266241 full-length cDNA:Ceres: 35056. 254521_at putative protein similar to unknown proteinAt5g44810 2.44 −1.09 0.041638 0.416086 (gb|AAC79139.1) 263419_atputative protein kinase contains a protein kinase At2g17220 2.43 1.090.008341 0.27009 domain profile (PDOC00100); supported by full- lengthcDNA: Ceres: 13257. 253323_at putative protein protein phosphatase Wip1,Homo At4g33920 2.43 −1.13 0.025096 0.456412 sapiens, PID: g2218063;supported by full-length cDNA: Ceres: 40123. 258983_at putativeaminotransferase similar to beta-alanine- At3g08860 2.42 1.14 0.0063310.051755 pyruvate aminotransferase GB: BAA19549 [Rattus norvegicus],alanine-glyoxylate aminotransferase GB: Q64565 [Rattus norvegicus]; PfamHMM hit: Aminotransferases class-III pyridoxal-phosphate 249583_atCALMODULIN-RELATED PROTEIN 2, TOUCH- At5g37770 2.42 −1.17 0.0063050.208762 INDUCED (TCH2); supported by full-length cDNA: Ceres: 25475.258046_at MAP kinase kinase 5 identical to GB: BAA28831 At3g21220 2.411.13 0.013633 0.416118 from [Arabidopsis thaliana]; supported by cDNA:gi_3219272_dbj_AB015316.1_AB015316 250990_at serine/threonine-specificprotein kinase NAK; At5g02290 2.41 −1.12 0.012886 0.320809 supported byfull-length cDNA: Ceres: 27477. 249423_at Expressed protein; supportedby full-length cDNA: At5g39785 2.41 −1.13 0.026115 0.657212 Ceres:118847. 248814_at putative protein similar to unknown protein At5g469102.4 −1.03 0.007949 0.787827 (pir||T06699) 254204_at putative proteinCGI-58 protein-Homo At4g24160 2.38 −1.04 0.010591 0.590709 sapiens, PID:g4929585 252485_at disease resistance protein RPP13-like proteinAt3g46530 2.37 −1.05 0.012107 0.677972 disease resistance proteinRPP8-Arabidopsis thaliana, EMBL: AF089710; supported by cDNA:gi_14334999_gb_AY037179.1_(—) 265620_at unknown protein At2g27310 2.35−1.2 0.049206 0.345125 264756_at receptor protein kinase (IRK1),putative similar to At1g61370 2.35 −1.07 0.010494 0.634376 receptorprotein kinase (IRK1) GI: 836953 from [Ipomoea trifida] 266993_atnodulin-like protein; supported by cDNA: At2g39210 2.33 1.12 0.0176360.371447 gi_16930478_gb_AF419593.1_AF419593 256735_at hypotheticalprotein predicted by genemark.hmm At3g29400 2.33 −1.12 0.006192 0.192654256425_at disease resistance protein, putative similar to diseaseAt1g33560 2.33 1.04 0.010206 0.488005 resistance protein RPP1-WsB GB:BAB01321 GI: 9279731 from (Arabidopsis thaliana) 250829_at diseaseresistance-like protein rpp8, Arabidopsis At5g04720 2.33 −1.08 0.0137210.38143 thaliana, EMBL: AF089711; supported by cDNA:gi_15292720_gb_AY050794.1_(—) 248698_at receptor-like protein kinase;supported by cDNA: At5g48380 2.33 1.13 0.021685 0.326459gi_13605826_gb_AF367312.1_AF367312 247594_at putative proteinfarnesylated protein GMFP5, At5g60800 2.33 1.37 0.027382 0.054007Glycine max, EMBL: U64916 266166_at putative glucosyltransferase;supported by full- At2g28080 2.32 −1.05 0.018474 0.764619 length cDNA:Ceres: 13761. 262745_at lipase, putative contains Pfam profile: PF00657At1g28600 2.32 −1.12 0.015545 0.267784 Lipase/Acylhydrolase withGDSL-like motif; supported by full-length cDNA: Ceres: 37307. 257407_atunknown protein At1g27100 2.32 −1.19 0.009875 0.068971 258282_at unknownprotein At3g26910 2.31 1.14 0.003241 0.168885 252373_at diseaseresistance protein EDS1; supported by At3g48090 2.31 −1.07 0.0119960.442811 cDNA: gi_15028150_gb_AY046025.1_(—) 250956_at putative proteinAt5g03210 2.31 −1.02 0.03092 0.993512 248851_s_at disease resistanceprotein-like; supported by cDNA: At5g46490 2.3 1.09 0.009234 0.638209gi_16323098_gb_AY057653.1_(—) 254924_at MAP kinase (ATMPK5) possibleinternal deletion At4g11330 2.29 −1.14 0.010478 0.330061 at position161, missing one A residue; reference GI: 457401; supported by cDNA:gi_457401_dbj_D21841.1_ATHATMPK5 250279_at ABA-responsive protein-likeABA-responsive At5g13200 2.29 −1.11 0.021853 0.295383 protein, Hordeumvulgare, EMBL: AF026538 263221_at UDP-galactose 4-epimerase-like proteinsimilar to At1g30620 2.28 1.23 0.015145 0.343241 proteins from manybacterial species including [Bacillus subtilis] and [Methanobacteriumthermoautotrophicum] 261718_at wall-associated kinase, putative similarto wall- At1g18390 2.28 1.07 0.008635 0.505026 associated kinase 2 GB:CAB42872 GI: 4826399 from [Arabidopsis thaliana] 250398_at putativeprotein predicted proteins, Arabidopsis At5g11000 2.28 1.16 0.0120150.299864 thaliana; supported by full-length cDNA: Ceres: 263168.256922_at hypothetical protein contains similarity to flavonol At3g190102.27 −1.04 0.029488 0.80973 synthase (FLS) GB: Q41452 from [Solanumtuberosum], contains Pfam profile: PF00671 Iron/Ascorbate oxidoreductasefamily; supported by full-length cDNA: Ceres: 41506. 267530_at putativereceptor-like protein kinase At2g41890 2.26 −1.11 0.028311 0.389366256627_at unknown protein; supported by cDNA: At3g19970 2.26 1.050.015238 0.715164 gi_14532501_gb_AY039875.1_(—) 255880_at hypotheticalprotein predicted by genscan+ At1g67060 2.26 −1.01 0.015412 0.926607254660_at receptor serine/threonine kinase-like protein At4g18250 2.26−1.06 0.024187 0.802259 receptor serine/threonine kinase PR5K, PATCHX:G1235680 264528_at hypothetical protein similar to Human XE169 At1g308102.25 1.03 0.00644 0.758062 protein (gi|3033385); similar to ESTgb|T88128 257784_at geranylgeranylated protein, putative similar toAt3g26970 2.25 1.17 0.00182 0.287058 ATGP4 GB: AAD00115 from[Arabidopsis thaliana] 255344_s_at putative receptor-like protein kinaseAt4g04540 2.25 1.01 0.022152 0.792265 255080_at arabinogalactan-proteinhomolog arabinogalactan- At4g09030 2.25 −1.04 0.036604 0.768432protein-Arabidopsis thaliana, PID: g3883126; supported by cDNA:gi_10880496_gb_AF195891.1_AF195891 259325_at unknown protein At3g053202.24 −1.15 0.016669 0.38111 252851_at putative protein CLATHRIN COATASSEMBLY At4g40080 2.24 −1.08 0.014274 0.543837 PROTEIN AP180-Musmusculus, SWISSPROT: Q61548; supported by full-length cDNA: Ceres: 8970.257071_at unknown protein; supported by cDNA: At3g28180 2.23 1.040.014928 0.697835 gi_15810494_gb_AY056286.1_(—) 253476_at S-receptorkinase-like protein serine/threonine- At4g32300 2.23 −1.04 0.0090960.440827 specific protein kinase PK10 precursor, Oryza sativa, PIR2:S50767 254292_at putative protein At4g23030 2.22 1.13 0.007331 0.570308249393_at disease resistance-like protein resistance gene Cf-4,At5g40170 2.22 −1.04 0.016127 0.647441 Lycopersicon hirsutum, EMBL:LHJ002235 249320_at disease resistance protein-like non-consensus TTAt5g40910 2.22 1.13 0.049144 0.285783 donor splice site at exon 1246327_at receptor-like serine/threonine kinase, putative similarAt1g16670 2.22 1.02 0.008469 0.775987 to receptor-like serine/threoninekinase GI: 2465923 from [Arabidopsis thaliana]; supported by cDNA:gi_16649102_gb_AY059921.1_(—) 267537_at putative guanylate kinase;supported by cDNA: At2g41880 2.21 −1.02 0.012268 0.883883gi_7861794_gb_AF204675.1_AF204675 251987_at CYTOCHROME P450 71B5;supported by cDNA: At3g53280 2.21 −1.27 0.010305 0.155225gi_3164131_dbj_D78601.1_D78601 248981_at regulatory protein NPR1-like;transcription factor At5g45110 2.21 1.11 0.020899 0.556465 inhibitor Ikappa B-like 265611_at unknown protein; supported by full-length cDNA:At2g25510 2.2 −1.04 0.010382 0.533642 Ceres: 10730. 259071_at unknownprotein similar to hin1 GB: CAA68848 At3g11650 2.2 −1.02 0.0088230.776008 [Nicotiana tabacum]; supported by cDNA:gi_9502173_gb_AF264698.1_AF264698 249029_at disease resistanceprotein-like At5g44870 2.2 1.01 0.033247 0.925701 265648_at putativebeta-1,3-glucanase; supported by full- At2g27500 2.19 −1.07 0.0157020.521836 length cDNA: Ceres: 1126. 252921_at putative protein DNAdamage-inducible protein- At4g39030 2.19 1.57 0.026714 0.071711Synechocystis sp., PIR2: S77364 266749_at putative protein kinasecontains a protein kinase At2g47060 2.18 −1.05 0.013372 0.636302 domainprofile (PDOC00100) 266231_at putative protein kinase At2g02220 2.18−1.01 0.008538 0.969684 254878_at heat shock transcription factor-likeprotein heat At4g11660 2.18 1.15 0.015925 0.386918 shock transcriptionfactor HSF29, Glycine max, PIR2: S59541 258764_at putativepectinesterase contains similarity to At3g10720 2.17 −1 0.01345 0.975443pectinesterase GB: AAB57671 [Citrus sinensis] 266975_at hypotheticalprotein predicted by grail At2g39380 2.16 1.09 0.019477 0.60417254921_at putative protein hypothetical protein F16G20.230- At4g113002.16 −1.01 0.016335 0.995903 Arabidopsis thaliana, PIR2: T05391;supported by full-length cDNA: Ceres: 17771. 259937_s_at putative ABCtransporter contains Pfam profile: At1g71330 2.14 1.25 0.009288 0.060426PF00005 ABC transporter 255524_at hypothetical protein similar topectinesterase At4g02330 2.14 −1.08 0.006633 0.352183 250018_at putativeprotein similar to unknown protein At5g18150 2.14 −1.05 0.0054270.652846 (emb|CAB87627.1) 249987_at putative protein predicted proteins,Arabidopsis At5g18490 2.14 1.03 0.016862 0.931777 thaliana; supported byfull-length cDNA: Ceres: 32414. 265722_at putative chlorophyll a/bbinding protein; supported At2g40100 2.13 1.35 0.029801 0.022089 byfull-length cDNA: Ceres: 6454. 262540_at hypothetical protein predictedby genemark.hmm At1g34260 2.13 1.1 0.022736 0.377889 264767_athypothetical protein similar to putative At1g61380 2.12 1.15 0.0124950.215443 serine/threonine kinase GI: 4585880 from [Arabidopsisthaliana]; supported by full-length cDNA: Ceres: 13461. 251192_at alphagalactosyltransferase-like protein alpha At3g62720 2.12 −1.11 0.01190.381401 galactosyltransferase-Trigonella foenum-graecum, EMBL:TFO245478; supported by cDNA: gi_15983425_gb_AF424587.1_AF424587249984_at putative protein rsc43, Dictyostelium discoideum, At5g184002.12 1.05 0.006326 0.639984 EMBL: AF011338; supported by full-lengthcDNA: Ceres: 6084. 249237_at putative protein similar to unknown proteinAt5g42050 2.12 1.01 0.019097 0.90689 (sp|P37707); supported byfull-length cDNA: Ceres: 6903. 249021_at putative protein similar tounknown protein At5g44820 2.12 −1.03 0.014955 0.780757 (pir||T04881)266452_at hypothetical protein predicted by genscan; supported At2g433202.11 1.01 0.010229 0.93189 by cDNA: gi_14517475_gb_AY039573.1_(—)266168_at putative protease inhibitor; supported by full-lengthAt2g38870 2.11 1.07 0.011954 0.24411 cDNA: Ceres: 11662. 257264_athypothetical protein contains Pfam profile: PF01657 At3g22060 2.11 1.410.033325 0.224965 Domain of unknown function; supported by cDNA:gi_14334417_gb_AY034900.1_(—) 252133_at hypothetical proteinhypothetical protein- At3g50900 2.11 −1.16 0.048974 0.506058 Arabidopsisthaliana chromosome 4 AP2 contig, PID: e353223; supported by full-lengthcDNA: Ceres: 10044. 248230_at putative protein similar to unknownprotein At5g53830 2.11 −1.24 0.009004 0.419028 (gb|AAF34839.1);supported by cDNA: gi_13926341_gb_AF372918.1_AF372918 247571_at snap25a;supported by full-length cDNA: At5g61210 2.11 1.1 0.033279 0.210386Ceres: 14562. 253147_at protein kinase-like protein serine/threonine-At4g35600 2.1 1.1 0.007538 0.342113 specific protein kinase APK1,Arabidopsis thaliana, PIR2: S28615 252976_s_at Phospholipase likeprotein Arabidopsis thaliana At4g38550 2.1 1.02 0.005166 0.820109 pEARLI4 mRNA, PID: g871782 260975_at receptor-like serine/threonine kinase,putative At1g53430 2.09 −1.06 0.02462 0.698322 similar to receptor-likeserine/threonine kinase GB: AAC50043 GI: 2465923 from [Arabidopsisthaliana] 256799_at unknown protein; supported by cDNA: At3g18560 2.091.14 0.021195 0.61081 gi_14190488_gb_AF380644.1_AF380644 246529_atserine/threonine-specific protein kinase-like protein At5g15730 2.091.07 0.010794 0.454295 serine/threonine-specific protein kinase NPK15-Nicotiana tabacum; supported by full-length cDNA: Ceres: 25636.245731_at MAP kinase, putative similar to MAP kinase kinase At1g735002.09 −1.17 0.002926 0.06007 5 GI: 3219273 from [Arabidopsis thaliana];supported by full-length cDNA: Ceres: 112118. 257785_atgeranylgeranylated protein, putative similar to At3g26980 2.08 1.120.027564 0.130143 ATGP4 GB: AAD00115 from [Arabidopsis thaliana]251248_at P-glycoprotein-like proetin P-glycoprotein-2- At3g62150 2.081.18 0.006349 0.219814 Arabidopsis thaliana, EMBL: Y10228 264841_atputative protein kinase similar to (Z71703), cdc2- At1g03740 2.07 1.030.009533 0.802311 like protein kinase; similar to ESTs gb|T20748,gb|T20464, and emb|Z17761; supported by cDNA: gi_14532735_gi_13430451262360_at receptor protein kinase, putative similar to receptorAt1g73080 2.07 1.07 0.049706 0.387954 protein kinase GI: 1389566 from[Arabidopsis thaliana] 249705_at serine/threonine protein kinase-likeAt5g35580 2.07 1.06 0.02776 0.584833 259876_at putative DnaJ proteinsimilar to dnaJ-like protein At1g76700 2.06 1.04 0.040672 0.74219 GB:CAA72705 [Arabidopsis thaliana]; Pfam HMM hit: DnaJ, prokaryotic heatshock protein 266316_at unknown protein; supported by cDNA: At2g270802.05 1.1 0.008877 0.282687 gi_15450380_gb_AY052291.1_(—) 262183_atunknown protein At1g77900 2.05 1.11 0.020307 0.383917 260345_at receptorprotein kinase, putative similar to receptor At1g69270 2.05 −1.160.02512 0.233028 protein kinase GI: 1389566 from (Arabidopsis thaliana);supported by cDNA: gi_4204848_gb_U55875.1_ATU55875 260635_at unknownprotein At1g62420 2.04 −1.19 0.00958 0.160716 253780_at proteinphosphatase 2C-like protein protein At4g28400 2.04 1.02 0.0490770.837741 phosphatase 2C-fission yeast, PIR2: S54297; supported by cDNA:gi_16604584_gb_AY059737.1_(—) 251218_at CP12 protein precursor-likeprotein CP12 protein At3g62410 2.04 1.05 0.005991 0.528908 precursor,chloroplast-Pisum sativum, PIR: T06562; supported by full-length cDNA:Ceres: 2721. 245641_at Expressed protein; supported by full-length cDNA:At1g25370 2.04 −1.04 0.0479 0.829103 Ceres: 118770. 263915_athypothetical protein predicted by genscan and At2g36430 2.03 −1.260.020455 0.076673 genefinder 254508_at putative protein gene F4P9.34chromosome II BAC At4g20170 2.03 −1.03 0.032001 0.79323 F4P9,Arabidopsis thaliana 253292_at Expressed protein; supported byfull-length cDNA: At4g33985 2.03 −1.02 0.00638 0.87138 Ceres: 9341.265772_at putative protein kinase contains a protein kinase At2g480102.02 1.04 0.012695 0.802318 domain profile (PDOC00100); supported bycDNA: gi_14335115_gb_AY037237.1_(—) 265375_at unknown protein; supportedby full-length cDNA: At2g06530 2.02 1.08 0.015552 0.48528 Ceres: 91878.265208_at putative giberellin beta-hydroxylase contains At2g36690 2.01−1.35 0.006868 0.034666 similarities to GA beta-20-hydroxylase fromtobacco (GB: 3327245) and to ethylene forming enzyme from Picea glauca(GB: L42466) 264746_at unknown protein similar to putative DNA-bindingAt1g62300 2.01 1.04 0.035415 0.469191 protein GI: 7268215 from[Arabidopsis thaliana]; supported by cDNA:gi_12658409_gb_AF331712.1_AF331712 260312_at putative disease resistanceprotein similar to disease At1g63880 2.01 −1.17 0.018521 0.24588resistance protein RPP1-WsC GB: AAC72979 [Arabidopsis thaliana]258173_at putative protein kinase similar to serine/threonine At3g216302.01 1.07 0.010988 0.529339 protein kinase Pto GB: AAB47421[Lycopersicon esculentum] (Plant Cell 9 (1), 61-73 (1997)) 247617_atreceptor like protein kinase receptor like protein At5g60270 2 −1.350.002662 0.065021 kinase, Arabidopsis thaliana, PIR: T47484 259213_atputative receptor ser/thr protein kinase similar to At3g09010 1.99 1.140.025161 0.261501 receptor kinase GB: S70769 [Arabidopsis thaliana];supported by full-length cDNA: Ceres: 124301. 258544_at diseaseresistance gene (RPM1) identical to disease At3g07040 1.99 −1.350.036667 0.073823 resistance gene (RPM1) GB: X87851 [Arabidopsisthaliana] 249777_at putative protein similar to unknown protein (gbAt5g24210 1.99 −1.11 0.022053 0.175713 AAD29063.1) 249208_at alleneoxide synthase (emb CAA73184.1); At5g42650 1.99 1.18 0.018657 0.090962supported by cDNA: gi_6002956_gb_AF172727.1_AF172727 248014_at putativeprotein similar to unknown protein At5g56340 1.99 −1.05 0.0453010.723728 (pir||T05064) 264223_s_at receptor kinase, putative similar toreceptor kinase 1 At1g67520 1.98 1.1 0.021718 0.628018 GI: 9294449 from[Arabidopsis thaliana] 262082_s_at wall-associated kinase 2, putativesimilar to At1g56120 1.98 1.12 0.030141 0.183617 receptor-likeserine/threonine kinase GB: AAC50043 GI: 2465923 from [Arabidopsisthaliana] 249835_s_at putative protein similar to unknown protein (gbAt5g23510 1.98 −1.08 0.01545 0.400133 AAF01580.1) 245051_at putativeWRKY-type DNA-binding protein; At2g23320 1.98 1.19 0.009782 0.0756supported by cDNA: gi_13506742_gb_AF224704.1_AF224704 264351_at unknownprotein Contains similarity to At1g03370 1.97 1.02 0.026436 0.91627gb|AB011110 KIAA0538 protein from Homo sapiens brain and tophospholipid-binding domain C2 PF|00168. ESTs gb|AA585988 and gb|T04384come from this gene 262926_s_at receptor kinase, putative similar toreceptor kinase 1 At1g65790 1.97 −1.11 0.021308 0.451766 [Brassica rapa]GB: BAA23676 253326_at putative protein polygalacturonase(EC 3.2.1.15)At4g33440 1.97 −1.05 0.019179 0.7895 precursor - Erwinia carotovora,PID: g42330 246305_at putative protein protein At2g40060 - ArabidopsisAt3g51890 1.97 1.2 0.016172 0.125232 thaliana, EMBL: AF002109; supportedby full-length cDNA: Ceres: 93427. 245219_at viral resistance protein,putative similar to viral At1g59124 1.97 −1.03 0.010527 0.805754resistance protein GI: 7110565 from [Arabidopsis thaliana] 267393_atsimilar to axi 1 protein from Nicotiana tabacum At2g44500 1.96 −1.240.025881 0.212221 259109_at putative serine threonine proteinphosphatase type At3g05580 1.96 1.08 0.029112 0.485226 one similar toGB: AAC39461 252037_at putative calmodulin calmodulin - TetrahymenaAt3g51920 1.96 1.1 0.015438 0.170162 pyriformis (SGC5), PIR1: MCTE;supported by cDNA: gi_14190470_gb_AF380635.1_AF380635 258176_at Bregulatory subunit of PP2A, putative similar to B At3g21650 1.95 −1.170.03792 0.249846 regulatory subunit of PP2A GB: AAB58902 [Arabidopsisthaliana] 256169_at receptor protein kinase, putative contains PfamAt1g51800 1.95 1.2 0.02536 0.076434 profiles: PF00069: Eukaryoticprotein kinase domain, multiple PF00560: Leucine Rich Repeat 260974_atreceptor-like serine/threonine kinase, putative At1g53440 1.94 −1.020.009705 0.677274 similar to receptor-like serine/threonine kinase GB:AAC50043 GI: 2465923 from [Arabidopsis thaliana] 252310_at GTPaseactivating-like protein GTPase activating At3g49350 1.94 −1 0.0267030.921316 protein gyp7, Yarrowia lipolytica, EMBL: YLGYP7 251790_atelicitor responsive/phloem-like protein FIERG2 At3g55470 1.94 1.050.012047 0.64204 protein, Oryza sativa, PIR: T04363 249480_s_at proteinkinase - like protein receptor-like protein At5g38990 1.94 −1.2 0.0195930.193368 kinase (EC 2.7.1.—) precursor, Madagascar periwinkle, PIR:T10060 249364_at putative protein predicted protein, ArabidopsisAt5g40590 1.94 −1.06 0.023463 0.5486 thaliana 265385_at putativediacylglycerol kinase; supported by full- At2g20900 1.93 1.03 0.023120.814052 length cDNA: Ceres: 15863. 264580_at unknown protein ESTgb|ATTS0295 comes from At1g05340 1.93 1.37 0.011774 0.077989 this gene;supported by full-length cDNA: Ceres: 20380. 258608_at unknown protein;supported by full-length cDNA: At3g03020 1.93 1.12 0.001615 0.228742Ceres: 35949. 262868_at unknown protein At1g64980 1.92 1.03 0.0100640.758096 260255_at putative protein kinase similar to p58 protein kinaseAt1g74330 1.92 −1.02 0.036098 0.867257 GB: AAB59449 (Homo sapiens);contains Pfam profile: PF00069 Eukaryotic protein kinase domain257902_at receptor kinase, putative similar to receptor kinase At3g284501.92 1.01 0.015158 0.903391 GB: AAD02501 from [Arabidopsis thaliana]254211_at phosphatase like protein phosphoprotein phosphatase At4g235701.92 1.08 0.021478 0.429462 (EC 3.1.3.16) PPT - rat 252009_at zincfinger - like protein zinc finger protein 216, At3g52800 1.92 1.010.025834 0.996803 Homo sapiens, EMBL: AF062072; supported by cDNA:gi_14596166_gb_AY042871.1_(—) 265460_at putative caltractin; supportedby full-length cDNA: At2g46600 1.91 −1.28 0.011693 0.060574 Ceres: 7802.262455_at Mlo protein, putative similar to Mlo protein At1g11310 1.91 −10.011858 0.991742 GB: Z83834 GI: 1877220 from [Hordeum vulgare];supported by full-length cDNA: Ceres: 259664. 262119_s_at glutathioneS-transferase, putative similar to At1g02930 1.91 1.13 0.011514 0.130465glutathione S-transferase GI: 860955 from [Hyoscyamus muticus];supported by cDNA: gi_15215607_gb_AY050332.1_(—) 257700_at unknownprotein similar to unknown protein At3g12740 1.91 1.12 0.011076 0.18275GB: AAD25612 from [Arabidopsis thaliana]; supported by full-length cDNA:Ceres: 37019. 253534_at cytochrome P450 monooxygenase; supported byAt4g31500 1.91 1.1 0.008445 0.216603 full-length cDNA: Ceres: 13745.248873_at disease resistance protein-like At5g46450 1.91 1.04 0.0193110.616452 251071_at putative protein receptor protein kinases At5g019501.89 −1.02 0.019672 0.77446 250419_at RPP1 disease resistance protein -like disease At5g11250 1.89 −1.16 0.007043 0.23803 resistance proteinRPP1-WsC, Arabidopsis thaliana, EMBL: AF098964 246018_at Expressedprotein; supported by full-length cDNA: At5g10695 1.88 1.11 0.0071660.390262 Ceres: 103171. 245151_at putative pectinesterase; supported byfull-length At2g47550 1.88 1.02 0.027515 0.828056 cDNA: Ceres: 111254.265499_at putative glucosyltransferase At2g15480 1.87 −1.11 0.0436770.508495 263797_at putative WRKY-type DNA binding protein; At2g245701.87 1.08 0.018452 0.267205 supported by cDNA:gi_15991743_gb_AF425836.1_AF425836 263731_at metalloproteinase, putativesimilar to At1g59970 1.87 −1.03 0.019632 0.713464 metalloproteinase GI:3128477 from [Arabidopsis thaliana] 252076_at LS1-like protein AT-LS1product - Arabidopsis At3g51660 1.87 1.38 0.021217 0.088589 thaliana,EMBL: X58827; supported by full-length cDNA: Ceres: 107294. 258460_atunknown protein At3g17330 1.86 1.07 0.005904 0.601401 245254_atATP-sulfurylase; supported by cDNA: At4g14680 1.86 −1.38 0.0316980.050397 gi_459143_gb_U06275.1_ATU06275 266536_at hypothetical proteinpredicted by genefinder; At2g16900 1.85 −1.07 0.006846 0.487008supported by cDNA: gi_14532491_gb_AY039870.1_(—) 265479_at hypotheticalprotein; supported by full-length At2g15760 1.85 −1.04 0.048838 0.747296cDNA: Ceres: 5. 262873_at hypothetical protein predicted by genemark.hmmAt1g64700 1.85 1.2 0.006355 0.233681 258207_at putative GTPpyrophosphokinase similar to GTP At3g14050 1.85 −1.03 0.021111 0.736124PYROPHOSPHOKINASE GB: O87331 from [Corynebacterium glutamicum];supported by cDNA: gi_7141305_gb_AF225703.1_AF225703 267335_s_atputative beta-1,3-glucanase At2g19440 1.84 −1.28 0.025894 0.194876245218_s_at viral resistance protein, putative, 5 partial similar toAt1g58842 1.84 −1.02 0.034348 0.880456 viral resistance protein GI:7110565 from [Arabidopsis thaliana] 264082_at unknown protein; supportedby full-length cDNA: At2g28570 1.83 1.16 0.032702 0.469306 Ceres: 36244.260037_at putative DNA-binding protein (RAV2-like) identical At1g688401.83 −1.21 0.029408 0.263089 to residues 34-352 of RAV2 GB: BAA34251(Arabidopsis thaliana); supported by full-length cDNA: Ceres: 19561.258134_at rubisco expression protein, putative similar to At3g24530 1.831.06 0.014418 0.42968 GB: O22034 from [Cyanidium caldarium] (J. PlantRes. 110, 235-245 (1997)); supported by full-length cDNA: Ceres: 148454.260314_at unknown protein similar to putative protein At1g63830 1.82−1.01 0.00932 0.923314 GB: CAA20468 [Arabidopsis thaliana] 258956_athypothetical protein predicted by At3g01440 1.82 −1.19 0.013406 0.260869genscan+; supported by full-length cDNA: Ceres: 13653. 262649_at unknownprotein contains similarity to xenotropic At1g14040 1.81 1.05 0.0099380.587887 and polytropic retrovirus receptor GB: 4759334 257972_atputative protein kinase, ATN1 almost identical (1 At3g27560 1.81 −1.040.029115 0.724347 amino acid) to GB: S61766 from [Arabidopsis thaliana];supported by cDNA: gi_16604327_gb_AY058062.1_(—) 250575_at putativeprotein At5g08240 1.81 1.08 0.022224 0.516011 259826_at armrepeat-containing protein, putative similar to At1g29340 1.8 1.010.02957 0.88125 GI: 2558938 from [Brassica napus] (Proc. Natl. Acad.Sci. U.S.A. 95 (1), 382-387 (1998)) 253364_at F-box protein family,AtFBX13 cotains similarity to At4g33160 1.8 1.01 0.015511 0.924255fimbriata GI: 547307 from [Antirrhinum majus] 248895_at receptor proteinkinase At5g46330 1.8 −1.03 0.014527 0.815519 263457_at unknown proteinAt2g22300 1.79 1.05 0.018298 0.6555 254553_at TMV resistance proteinN-like TMV resistance At4g19530 1.79 −1.02 0.024648 0.800063 protein N,Nicotiana glutinosa, PIR2: A54810 254331_s_at cytochrome P450-likeprotein flavonoid 3,5- At4g22710 1.79 1.04 0.011357 0.507737 hydroxylaseHf1, Petunia x hybrida, PIR2: S38985 245838_at disease resistanceprotein, putative similar to disease At1g58410 1.79 1.04 0.0452410.800057 resistance protein RPP8 GI: 8843900 from [Arabidopsis thaliana]267392_at putative beta-glucosidase At2g44490 1.78 −1.01 0.012930.768374 264879_at cotton fiber expressed protein, putative similar toAt1g61260 1.78 −1.08 0.020899 0.6028 cotton fiber expressed protein 1GI: 3264828 from [Gossypium hirsutum] 251804_at beta-1,3-glucanase -like protein probable beta-1,3- At3g55430 1.78 −1.02 0.033278 0.91732glucanase, Triticum aestivum, PIR: T06268; supported by full-lengthcDNA: Ceres: 8980. 249314_at receptor kinase-like protein At5g41180 1.781.15 0.034221 0.348074 245456_at disease resistance RPP5 like proteinAt4g16950 1.78 −1.02 0.014799 0.787739 267169_at putative oxidoreductaseAt2g37540 1.77 1.01 0.020016 0.912423 265079_at hypothetical proteincontains similarity to zinc finger At1g55460 1.76 −1.02 0.015429 0.82749protein rts2 GB: U16133 GI: 563244 from [Saccharomyces cerevisiae];supported by cDNA: gi_13430439_gb_AF360132.1_AF360132 259230_at unknownprotein; supported by cDNA: At3g07780 1.76 1.13 0.012523 0.041915gi_15028084_gb_AY045899.1_(—) 250850_at putative protein; supported bycDNA: At5g04550 1.76 −1.14 0.015093 0.108003gi_13605828_gb_AF367313.1_AF367313 261506_at choline kinase, putativesimilar to At1g71697 1.75 1.03 0.033638 0.818348 CHOLINE/ETHANOLAMINEKINASE GB: Q9Y259 from [Homo sapiens] 251028_at putative proteinputative hydrolase At2g32150- At5g02230 1.75 −1.06 0.019924 0.548891Arabidopsis thaliana, EMBL: AC006223; supported by full-length cDNA:Ceres: 36724. 258336_at putative ethylene-inducible protein similar toAt3g16050 1.74 1.13 0.019656 0.136759 ethylene-inducible protein GB:M88254 from [Hevea brasiliensis]; supported by cDNA:gi_4103951_gb_AF029980.1_AF029980 253415_at putative proteinpeptidyl-prolyl cis-trans isomerase, At4g33060 1.74 1.15 0.0229330.090678 Schizosaccharomyces pombe, gb: SPBC16H5 251643_at guanylatekinase-like protein guanylate kinase - At3g57550 1.74 1.12 0.0146590.125227 Mus musculus, TREMBL: MMU53514_1; supported by cDNA:gi_7861797_gb_AF204676.1_AF204676 247384_at protein kinase; supported bycDNA: At5g63370 1.74 1.11 0.010852 0.400409gi_16974578_gb_AY060555.1_(—) 265269_at hypothetical protein predictedby genscan At2g42950 1.72 1.09 0.017878 0.365888 262571_at hypotheticalprotein predicted by genscan+; At1g15430 1.72 1.12 0.022912 0.305054supported by cDNA: gi_15293248_gb_AY051058.1_(—) 259466_at responseregulator 5, putative similar to response At1g19050 1.72 −1.03 0.0267290.64387 regulator 5 GI: 3953599 from [Arabidopsis thaliana]; supportedby cDNA: gi_3953602_dbj_AB008490.1_AB008490 254723_at ammonium transportprotein (AMT1); supported by At4g13510 1.72 1.08 0.011754 0.406577 cDNA:gi_14335079_gb_AY037219.1_(—) 253193_at putative protein SEC7 protein,Saccharomyces At4g35380 1.72 1.12 0.019937 0.504827 cerevisiae, PIR2:S49764 265461_at unknown protein similarity to ubiquitin family ofAt2g46500 1.71 1.18 0.019691 0.111325 proteins; supported by cDNA:gi_16930424_gb_AF419566.1_AF419566 253614_at putative protein heat shockprotein 101 - Triticum At4g30350 1.71 −1.07 0.030479 0.677967 aestivum,PID: g4558484 247816_at similar to unknown protein (pir||S75584);supported At5g58260 1.71 −1.12 0.011236 0.191707 by full-length cDNA:Ceres: 3488. 262457_at hypothetical protein similar to hypotheticalprotein At1g11200 1.7 −1.03 0.017609 0.719233 GB: CAB36801 GI: 4455265from [Arabidopsis thaliana]; supported by full-length cDNA: Ceres:40975. 255512_at Expressed protein; supported by cDNA: At4g02195 1.691.06 0.014636 0.692316 gi_5059351_gb_AF154574.1_AF154574 251516_s_atputative protein hypothetical protein SPCC320.08 - At3g59310 1.69 −1.060.017534 0.387516 Schizosaccharomyces pombe, PIR: T41303 254103_atputative protein; supported by full-length cDNA: At4g25030 1.68 1.040.007754 0.433098 Ceres: 16463. 245757_at phosphate-induced (phi-1)protein, putative similar At1g35140 1.68 −1.51 0.004633 0.081204 tophi-1 GB: BAA33810 GI: 3759184 from [Nicotiana tabacum]; supported byfull-length cDNA: Ceres: 118937. 253387_at P-Protein-like proteinP-Protein precursor, Solanum At4g33010 1.66 1.04 0.019086 0.463263tuberosum, gb: Z99770; supported by cDNA: gi_14596024_gb_AY042800.1_(—)247272_at GTP cyclohydrolase II; 3,4-dihydroxy-2-butanone-4- At5g643001.66 1 0.011375 0.888475 phoshate synthase (emb|CAA03884.1) supported bycDNA: gi_940382_dbj_D45165.1_ATHGTPCII 261788_at unknown protein;supported by full-length cDNA: At1g15980 1.65 −1.05 0.013373 0.66035Ceres: 122986. 249010_at unknown protein; supported by cDNA: At5g445801.65 1.05 0.008905 0.282782 gi_15027902_gb_AY045808.1_(—) 259074_atputative protein kinase contains Pfam profile: At3g02130 1.63 −1.030.007959 0.571341 Eukaryotic protein kinase domain 258394_at unknownprotein; supported by full-length cDNA: At3g15530 1.63 1.07 0.0042840.548019 Ceres: 15303. 258665_at thioredoxin-like protein similar tothioredoxin H- At3g08710 1.61 1.03 0.0083 0.731007 type GB: P29448[Arabidopsis thaliana] 253317_at putative protein At4g33960 −1.83 −1.770.010341 0.022397 260126_at putative hydroxymethyltransferase similar toserine At1g36370 −1.93 −1.86 0.005701 0.006964 hydroxymethyltransferageGB: P50433 from [Solanum tuberosum]; supported by full-length cDNA:Ceres: 122515. 246926_at putative protein At5g25240 −2.09 −2.21 0.0196030.017979 258217_at unknown protein contains Pfam profile PF00398At3g17990 −2.21 −2.27 0.009887 0.0037 Ribosomal RNA adenine dimethylases258218_at methyltransferase, putative similar to At3g18000 −2.21 −2.290.00667 0.009294 methyltransferase GB: AAC01738 from [Amycolatopsismediterranei] 254343_at PRH26 protein; supported by full-length cDNA:At4g21990 −2.22 −1.83 0.012838 0.031291 Ceres: 36866. 265121_at similarto flavin-containing monooxygenase At1g62560 −2.37 −1.87 0.0201260.00922 (sp|P36366); similar to ESTs gb|R30018, gb|H36886, gb|N37822,and gb|T88100 similar to flavin- containing monooxygenase GB: AAA21178GI: 349534 from [Oryctolagus cuniculus]; supported by cDNA:gi_13877746_gb_AF37013 251039_at putative protein hypothetical proteinT6H20.90 - At5g02020 −3.73 −1.91 0.001899 0.021967 Arabidopsis thaliana,EMBL: AL096859; supported by cDNA: gi_16648747_gb_AY058150.1_(—)259015_at unknown protein similar to hypothetical protein At3g07350−3.79 −1.81 0.001762 0.010373 GB: AAC17612 [Arabidopsis thaliana];supported by full-length cDNA: Ceres: 251012. 248676_at putative proteinsimilar to unknown protein At5g48850 −5.55 −4.23 0.003428 0.003335(gb|AAC72543.1) 249752_at putative protein similar to unknown protein(emb At5g24660 −5.87 −2.27 0.002654 0.005949 CAB62461.1); supported byfull-length cDNA: Ceres: 268701. 246935_at leucine-rich repeatscontaining protein grr1 - At5g25350 −1.64 −1.09 0.01077 0.205242 Glycinemax. EMBL: AF019910 261957_at methionine/cystathionine gamma lyase,putative At1g64660 −1.66 1.1 0.017509 0.258584 similar to methioninegamma-lyase GB: CAA04124.1 GI: 2330885 from [Trichomonas vaginalis];supported by cDNA: gi_15450931_gb_AY054546.1_(—) 263284_at unknownprotein At2g36100 −1.68 1.21 0.009385 0.046069 263064_at putative bZIPtranscription factor contains a bZIP At2g18160 −1.68 −1.04 0.0037050.553739 transcription factor basic domain signature (PDOC00036);supported by cDNA: gi_14335073_gb_AY037216.1_(—) 265102_at putativeperoxidase similar to cationic peroxidase At1g30870 −1.69 1.01 0.0085340.760053 (gi|1232069); similar to EST gb|AI100412; supported byfull-length cDNA: Ceres: 123968. 259773_at auxin-induced protein,putative similar to At1g29500 −1.69 1.03 0.017479 0.683467 SP: P33083from [Glycine max] 258181_at nitrate transporter identical to nitratetransporter At3g21670 −1.7 −1.68 0.013713 0.025046 GB: CAB38706[Arabidopsis thaliana]; supported by full-length cDNA: Ceres: 111089.252220_at putative protein hypothetical protein - Arabidopsis At3g49940−1.7 −1.08 0.010242 0.277047 thaliana, EMBL: CAB38293; supported byfull-length cDNA: Ceres: 17840. 251524_at 3-isopropylmalatedehydratase-like protein (small At3g58990 −1.71 −1.3 0.015617 0.116619subunit) 3-isopropylmalate dehydratase, small subunit - Thermotogamaritima, PIR: A72363 258008_at putative late embryogenesis abundantprotein similar At3g19430 −1.72 1.26 0.007578 0.089324 to GB: AAB01570from [Picea glauca] 263227_at Expressed protein; supported by cDNA:At1g30750 −1.73 1.1 0.00931 0.284316 gi_15292976_gb_AY050922.1_(—)263118_at putative 3-methylcrotonyl-CoA carboxylase ESTs At1g03090 −1.73−1.22 0.009453 0.064506 gb|H35836, gb|AA651295 and gb|AA721862 come fromthis gene; supported by cDNA: gi_533706_gb_U12536.1_ATU12536 248252_atputative protein similar to unknown protein At5g53250 −1.73 1.160.005785 0.142465 (emb|CAB71094.1) 256598_at cytochrome P450 homolog,putative similar to At3g30180 −1.74 1.01 0.019165 0.939678 cytochromeP450 homolog GB: U54770 GI: 1421740 from [Lycopersicon esculentum];supported by full- length cDNA: Ceres: 11278. 256062_at unknown protein;supported by full-length cDNA: At1g07090 −1.75 1.03 0.007971 0.599694Ceres: 28780. 263490_at F-box protein ORE9, AtFBL7 identical to F-boxAt2g42620 −1.76 1.14 0.014384 0.078788 containing protein ORE9 GI:15420162 from [Arabidopsis thaliana] 247477_at putative protein 21Kprotein precursor, Medicago At5g62340 −1.76 1.03 0.019734 0.869872sativa, PIR: T09390 262399_at unknown protein; supported by full-lengthcDNA: At1g49500 −1.77 −1.05 0.018923 0.609256 Ceres: 33047. 259856_atunknown protein; supported by full-length cDNA: At1g68440 −1.77 −1.410.017035 0.048737 Ceres: 34166. 253510_at hypothetical protein At4g31730−1.77 1.29 0.034578 0.053073 251017_at protein phosphatase - likeprotein protein At5g02760 −1.77 −1.04 0.007317 0.502031 phosphatase 2Chomolog, Mesembryanthemum crystallinum, EMBL: AF097667 248279_atputative protein similar to unknown protein At5g52910 −1.77 −1.280.016383 0.116964 (pir||T13959) 266191_at putative peroxidase At2g39040−1.78 1.26 0.012061 0.114533 253217_at actin depolymerizing factor -like protein actin At4g34970 −1.78 1.31 0.011164 0.086098 depolymerizingfactor1, Arabidopsis thaliana, PID: G1408471 262717_s_at putativecytochrome P450 similar to gb|AF069494 At1g16410 −1.79 −1.32 0.0169050.014389 cytochrome P450 from Sinapis alba and is a member of thePF|00067 Cytochrome P450 family. EST gb|F14190 comes from this gene;supported by cDNA: gi_15208670_gb_AY035021.2_(—) 262517_at putativeglutathione transferase Second of three At1g17180 −1.79 1.02 0.020660.906386 repeated putative glutathione transferases. 72% identical toglutathione transferase [Arabidopsis thaliana] (gi|4006934). Location ofests 191A10T7 (gb|R90188) and 171N13T7 (gb|R65532) 256926_athypothetical protein predicted by genemark.hmm At3g22540 −1.79 1.210.036851 0.289954 256252_at glucosyl transferase, putative similar tozeatin O- At3g11340 −1.79 1.59 0.019921 0.01385 xylosyltransferase SP:P56725 [Phaseolus vulgaris (Kidney bean) (French bean)] 261226_atexpansin S2 precursor, putative similar to At1g20190 −1.8 −1.05 0.0126550.608442 GB: U30460 from [Cucumis sativus]; supported by full-lengthcDNA: Ceres: 11011. 251144_at anthranilate N-benzoyltransferase-likeprotein At5g01210 −1.8 1.11 0.008524 0.106988 anthranilateN-benzoyltransferase, clove pink, PIR: T10717; supported by cDNA:gi_15912268_gb_AY056412.1_(—) 265645_at unknown protein At2g27370 −1.811.1 0.025976 0.504975 249923_at conglutin gamma-like protein conglutingamma At5g19120 −1.81 −1.05 0.007868 0.519593 precursor, Lupinusangustifolius, PIR: S21426; supported by cDNA:gi_15010797_gb_AY045700.1_(—) 247914_at xyloglucan endotransglycosylaseAt5g57540 −1.81 −1.03 0.026871 0.814009 265048_at jasmonate inducibleprotein, putative similar to At1g52050 −1.82 1.15 0.022645 0.325821jasmonate inducible protein GI: 9279642 from [Arabidopsis thaliana]252970_at small auxin up RNA (SAUR-AC1); supported by At4g38850 −1.821.19 0.007042 0.093178 full-length cDNA: Ceres: 14973. 249862_at PGPD14protein; supported by full-length cDNA: At5g22920 −1.82 −1.2 0.0133350.024948 Ceres: 41666. 266820_at putative AP2 domain transcriptionfactor pFAM At2g44940 −1.84 −1.27 0.027529 0.279728 domain (PF00847)supported by full-length cDNA: Ceres: 31044. 258038_at unknown protein;supported by full-length cDNA: At3g21260 −1.84 −1.25 0.024483 0.131574Ceres: 260109. 252250_at putative protein predicted protein, ArabidopsisAt3g49790 −1.85 −1.2 0.011715 0.131586 thaliana 247337_at putativeprotein similar to unknown protein At5g63660 −1.85 1 0.021642 0.941607(pir||S51637) 260167_at hypothetical protein predicted by genscan+At1g71970 −1.86 −1.06 0.02425 0.744455 257162_s_at ammonium transporter,putative similar to At3g24290 −1.86 −1.03 0.01777 0.655292 GB: AAD54638from [Arabidopsis thaliana] (Plant Cell (1999) 11 (5), 937-948)246275_at putative protein; supported by full-length cDNA: At4g36540−1.86 1.06 0.011645 0.640095 Ceres: 123997. 245586_at hypotheticalprotein At4g14980 −1.86 1.16 0.037731 0.349881 245136_at putativeauxin-regulated protein At2g45210 −1.86 1.1 0.020869 0.28948 262850_atsignal response protein (GAI) identical to GAI At1g14920 −1.87 −1.050.012647 0.589803 GB: CAA75492 GI: 2569938 [Arabidopsis thaliana] (GenesDev. In press); supported by cDNA: gi_16648833_gb_AY058194.1_(—)258080_at unknown protein; supported by full-length cDNA: At3g25930−1.87 1.11 0.025451 0.601329 Ceres: 2767. 253255_at putativeauxin-regulated protein auxin-induced At4g34760 −1.87 −1.2 0.0076830.154545 protein X15, Glycine max, PIR2: JQ1097; supported byfull-length cDNA: Ceres: 10510. 246996_at putative protein similar tounknown protein At5g67420 −1.87 −1.17 0.029109 0.184764(emb|CAB62102.1); supported by full-length cDNA: Ceres: 40250. 265511_atputative glycine-rich protein; supported by cDNA: At2g05540 −1.88 −1.360.004653 0.037214 gi_15215617_gb_AY050337.1_(—) 264957_at F-box proteinfamily, AtFBL5 contains similarity to At1g77000 −1.88 −1.06 0.0215050.577258 F-box protein FBL2 GI: 6063090 from [Homo sapiens]; supportedby full-length cDNA: Ceres: 3549. 264467_at unknown protein similar toEST At1g10140 −1.88 1.26 0.012415 0.023258 gb|AA598098; supported byfull-length cDNA: Ceres: 23916. 256828_at unknown protein At3g22970−1.88 1.18 0.017776 0.232803 248178_at root cap protein 2-like proteinAt5g54370 −1.88 1.29 0.00898 0.087446 262396_at unknown protein;supported by full-length cDNA: At1g49470 −1.89 −1.17 0.02115 0.065156Ceres: 95546. 259976_at hypothetical protein; supported by full-lengthAt1g76560 −1.89 −1.22 0.011496 0.142412 cDNA: Ceres: 147838. 252834_atputative protein RING-H2 zinc finger protein ATL6- At4g40070 −1.89 1.240.030751 0.235116 Arabidopsis thaliana, PID: g4928403; supported bycDNA: gi_16930492_gb_AF419600.1_AF419600 250860_at amino acidtransport-like protein amino acid At5g04770 −1.89 −1.19 0.02117 0.317647transport protein AAT1, Arabidopsis thaliana, PIR: S51171; supported byfull-length cDNA: Ceres: 158156. 265049_at jasmonate inducible protein,putative similar to At1g52060 −1.9 1.31 0.010222 0.06857 jasmonateinducible protein GI: 9279642 from [Arabidopsis thaliana] 265050_atjasmonate inducible protein, putative similar to At1g52070 −1.91 1.320.019022 0.277021 jasmonate inducible protein GI: 9279641 from[Arabidopsis thaliana] 252991_at protein kinase like protein proteinkinase 6 (EC At4g38470 −1.91 −1.43 0.022882 0.053733 2.7.1.—)-soybean,PIR2: S29851 250157_at prx10 peroxidase-like protein prx10 peroxidase,At5g15180 −1.91 1.05 0.009746 0.667075 Spinacia oleracea, EMBL: SOY16776267457_at putative proline-rich protein At2g33790 −1.92 1.55 0.026880.053166 266882_at unknown protein; supported by full-length cDNA:At2g44670 −1.92 −1.35 0.00935 0.103065 Ceres: 40641. 263208_at zincfinger protein 5, ZFP5 possible transcription At1g10480 −1.93 1.060.009367 0.572822 factor with C2H2 zinc finger; supported by full-length cDNA: Ceres: 23664. 253722_at putative protein zinc fingertranscription factor- At4g29190 −1.93 1.08 0.004592 0.184244 Arabidopsisthaliana, PID: g2961542; supported by full-length cDNA: Ceres: 16432.251356_at putative protein hypothetical proteins-Arabidopsis At3g61060−1.93 −1.13 0.007848 0.181064 thaliana; supported by cDNA:gi_14334587_gb_AY034967.1_(—) 245176_at unknown protein similar toGP|2104534|AF001308 At2g47440 −1.93 −1.64 0.031285 0.016259 (T10M13.11)262170_at hypothetical protein predicted by At1g74940 −1.94 1.090.007492 0.34681 genemark.hmm; supported by full-length cDNA: Ceres:24864. 260900_s_at branched-chain alpha keto-acid dehydrogenase,At1g21400 −1.94 −1.33 0.003536 0.091842 putative similar tobranched-chain alpha keto-acid dehydrogenase GB: AAC69851 GI: 3822223from [Arabidopsis thaliana] 260058_at unknown protein; supported bycDNA: At1g78100 −1.94 1.22 0.026338 0.07061gi_15450975_gb_AY054568.1_(—) 259854_at RING-H2 zinc finger proteinATL3, putative similar At1g72200 −1.94 1.07 0.006318 0.364739 to GI:4928397 from [Arabidopsis thaliana] (Plant Mol. Biol. 40 (4), 579-590(1999)) 258145_at integral membrane protein, putative similar toAt3g18200 −1.94 1.08 0.032913 0.537375 MtN21 (nodulation-induced gene)GB: CAA75575 [Medicago truncatula] 253763_at xyloglucanendotransglycosylase-like protein At4g28850 −1.94 −1.07 0.0104030.604484 xyloglucan endotransglycosylase 1, Fagus sylvatica, PID:e1354157 249008_at putative protein contains similarity to DNA-3-At5g44680 −1.94 1.04 0.019733 0.431852 methyladenine glycosylase I;supported by full-length cDNA: Ceres: 29551. 261711_at unknown proteinsimilar to hypothetical protein At1g32700 −1.95 −1.07 0.022252 0.357576GB: AAF25968 GI: 6714272 from [Arabidopsis thaliana]; supported byfull-length cDNA: Ceres: 206224. 260887_at ascorbate oxidasepromoter-binding protein, putative At1g29160 −1.95 −1.05 0.0087730.547417 similar to ascorbate oxidase promoter-binding protein GB:D45066 GI: 853689 from [Cucurbita maxima] 254718_at putative proteindisease resistance response protein At4g13580 −1.95 1.13 0.0081660.148335 206-d, Pisum sativum, U11716 253103_at putative auxin-inducedprotein high similarity to At4g36110 −1.95 1.24 0.007143 0.125412auxin-induced protein 15A, soybean, PIR2: JQ1096; supported by cDNA:gi_13194817_gb_AF349524.1_AF349524 245987_at NAM-like proteinhypothetical protein SENU5, At5g13180 −1.95 −1 0.030979 0.994604senescence up-regulated-Lycopersicon esculentum, EMBL: Z75524; supportedby cDNA: gi_14326559_gb_AF385734.1_AF385734 264130_at hypotheticalprotein predicted by genemark.hmm At1g79160 −1.96 −1.01 0.0076030.925019 257076_at unknown protein At3g19680 −1.96 −1.32 0.006420.015347 248564_at putative protein contains similarity to AT-hookAt5g49700 −1.96 1.11 0.017313 0.355178 DNA-binding protein 246228_atperoxidase like protein At4g36430 −1.96 1.3 0.014156 0.048404 245090_atputative integral membrane protein nodulin At2g40900 −1.96 1.07 0.0231570.443533 265031_at serine/threonine protein kinase, putative similar toAt1g61590 −1.97 1.11 0.0313 0.357745 serine/threonine protein kinase GI:1066501 from [Arabidopsis thaliana] 263981_at unknown protein; supportedby full-length cDNA: At2g42870 −1.97 −1.13 0.013425 0.350209 Ceres:102453. 252570_at isovaleryl-CoA-dehydrogenase precursor (IVD);At3g45300 −1.97 −1.07 0.015973 0.428779 supported by full-length cDNA:Ceres: 33674. 248432_at putative protein similar to unknown proteinAt5g51390 −1.97 −1.14 0.006297 0.177565 (gb|AAB68039.1); supported byfull-length cDNA: Ceres: 1076. 267628_at unknown protein similar toGP|2262147|AC002330 At2g42280 −1.98 1.01 0.023113 0.929253 266941_atperoxidase (ATP22a) identical to GB: Y08781 At2g18980 −1.98 −1.160.014024 0.253565 266838_at similar to jasmonate-inducible proteins fromAt2g25980 −1.98 1.03 0.013791 0.844383 Brassica napus 263318_atExpressed protein; supported by full-length cDNA: At2g24762 −1.98 1.020.019425 0.816736 Ceres: 19631. 260081_at unknown protein At1g78170−1.98 1.1 0.010912 0.443013 257654_at DnaJ protein, putative containsPfam profile: At3g13310 −1.98 1.19 0.018497 0.11787 PF00226 DnaJ domain;supported by full-length cDNA: Ceres: 31309. 257294_at non-phototropichypocotyl protein, putative similar At3g15570 −1.98 −1.4 0.0175940.029437 to GB: AAF05914 from [Arabidopsis thaliana]; supported byfull-length cDNA: Ceres: 118259. 254606_at nodulin-26-like protein majorintrinsic protein, At4g19030 −1.98 1.03 0.008673 0.680712 Oryza sativa,PIR2: S52003; supported by full-length cDNA: Ceres: 109513. 264014_atputative auxin-regulated protein At2g21210 −1.99 −1.17 0.002926 0.036113260770_at RING-H2 finger protein RHA3a, putative similar to At1g49200−1.99 1.24 0.024855 0.128926 RING-H2 finger protein RHA3a GI: 3790573from [Arabidopsis thaliana]; supported by cDNA:gi_14517431_gb_AY039551.1_(—) 260693_at peptide transporter PTR2-B,putative similar to At1g32450 −1.99 −1 0.029791 0.955651 SP: P46032 from[Arabidopsis thaliana] 257448_s_at putative protein various predictedproteins At3g45800 −1.99 −1.12 0.018199 0.206911 Arabidopsis thaliana259328_at putative lectin contains Pfam profile: PF01419 At3g16440 −21.24 0.010314 0.191237 jacalin-like lectin domain; similar to jasmonateinducible protein GB: Y11483 (Brassica napus), myrosinase bindingprotein GB: BAA84545 (Arabidopsis thaliana); supported by cDNA:gi_6694742_gb_AF214573.1_AF2145 263151_at hypothetical protein predictedby At1g54120 −2.01 −1.32 0.026676 0.072957 genemark.hmm; supported byfull-length cDNA: Ceres: 94743. 262427_s_at thioglucosidase, putativesimilar to thioglucosidase At1g47600 −2.01 1.2 0.008411 0.161898 GI:871992 from [Arabidopsis thaliana] 261822_at unknown protein; supportedby full-length cDNA: At1g11380 −2.01 −1.42 0.035581 0.129626 Ceres:113571. 265245_at unknown protein At2g43060 −2.03 −1.03 0.0105590.598558 258511_at unknown protein; supported by full-length cDNA:At3g06590 −2.03 −1.06 0.005721 0.306173 Ceres: 9391. 251072_at putativeprotein wound-inducible protein wun1 At5g01740 −2.03 −1.26 0.0239910.03577 protein-Solanum tuberosum, PIR: JQ0398; supported by full-lengthcDNA: Ceres: 248967. 267178_at unknown protein; supported by full-lengthcDNA: At2g37750 −2.04 1.3 0.011938 0.023415 Ceres: 28529. 262236_athypothetical protein similar to hypothetical protein At1g48330 −2.04−1.17 0.028943 0.116441 GI: 9294146 from [Arabidopsis thaliana]250717_at putative protein similar to unknown protein At5g06200 −2.041.1 0.014766 0.475991 (gb|AAF00668.1) 263265_at hypothetical proteinpredicted by genscan and At2g38820 −2.05 −1.04 0.028413 0.735506genefinder; supported by cDNA: gi_16649128_gb_AY059934.1_(—) 263150_atheat-shock protein, putative similar to heat-shock At1g54050 −2.05 1.30.019374 0.275131 protein GI: 472939 from [Helianthus annuus]; supportedby full-length cDNA: Ceres: 97415. 254820_s_at pEARLI 1-like proteinArabidopsis thaliana At4g12510 −2.05 1.07 0.00646 0.52646 pEARLI 1 mRNA,completecds, PID: g871780 251174_at putative protein latex proteinallergen Hev b 7- At3g63200 −2.05 −1.09 0.011679 0.253402 Heveabrasiliensis, EMBL: AF113546; supported by cDNA:gi_15912226_gb_AY056391.1_(—) 250469_at pollen allergen-like proteinSAH7 protein, At5g10130 −2.05 −1.05 0.021086 0.612309 Arabidopsisthaliana, EMBL: ATH133639 249606_at putative protein DNA-binding proteinCCA1, At5g37260 −2.05 1.11 0.011138 0.453754 Arabidopsis thaliana, PIR:T02684 252368_at cytochrome P450-like protein cytochrome P450 At3g48520−2.06 1.18 0.017948 0.40172 CYP94A1-Vicia sativa, PIR2: T08014 245277_atglucosyltransferase like protein; supported by At4g15550 −2.07 −1.210.004725 0.325423 cDNA: gi_2149126_gb_U81293.1_ATU81293 260266_atputative B-box zinc finger protein contains Pfam At1g68520 −2.08 −1.060.023551 0.259093 profile: PF00643 B-box zinc finger; supported byfull-length cDNA: Ceres: 108109. 260741_at hypothetical protein containsPfam profile: PF00117 At1g15045 −2.09 1.12 0.016477 0.263068 Glutamineamidotransferase class-I 257858_at hypothetical protein predicted byAt3g12920 −2.1 1 0.019142 0.98788 genefinder; supported by full-lengthcDNA: Ceres: 924. 266372_at putative two-component response regulator 3At2g41310 −2.11 −1.24 0.013281 0.195422 protein identical to GB:AB010917, contains a response regulator receiver domain; supported bycDNA: gi_3273199_dbj_AB010917.1_AB010917 266072_at putativetrehalose-6-phosphate synthase At2g18700 −2.11 −1.08 0.005616 0.502618255858_at zinc finger protein (ZFP6) identical to zinc finger At1g67030−2.11 1.3 0.017196 0.066902 protein GI: 790683 from [Arabidopsisthaliana]; supported by cDNA: gi_15215716_gb_AY050387.1_(—) 247954_atbeta-galactosidase (emb|CAB64740.1); supported At5g56870 −2.12 −1.360.01322 0.072012 by cDNA: gi_15451017_gb_AY054589.1_(—) 252036_atputative protein; supported by full-length cDNA: At3g52070 −2.13 −1.210.011681 0.137087 Ceres: 118329. 258497_at putative flowering-time geneCONSTANS (COL2) At3g02380 −2.14 −1.47 0.018979 0.03124 identical toputative flowering-time gene CONSTANS (COL2) GB: AAB67879 GI: 1507699(Arabidopsis thaliana); supported by full-length cDNA: Ceres: 949.253829_at Medicago nodulin N21-like protein MtN21 gene, At4g28040 −2.14−1.2 0.006927 0.185535 Medicago truncatula, Y15293; supported by cDNA:gi_13899060_gb_AF370525.1_AF370525 248801_at homeobox-leucine zipperprotein-like; supported by At5g47370 −2.14 1.06 0.008347 0.456353 cDNA:gi_15450446_gb_AY052324.1_(—) 247921_at CONSTANS-like B-box zinc fingerprotein-like; At5g57660 −2.14 −1.13 0.003117 0.120344 supported byfull-length cDNA: Ceres: 6639. 257615_at unknown protein At3g26510 −2.16−1.13 0.004838 0.273425 266140_at nodulin-like protein; supported bycDNA: At2g28120 −2.17 −1.3 0.008244 0.055633gi_16209713_gb_AY057618.1_(—) 257643_at AP2 domain transcription factorcontains Pfam At3g25730 −2.17 −1.32 0.038334 0.152701 profile: PF00847AP2 domain; similar to RAV1 (DNA-binding protein) GB: BAA34250[Arabidopsis thaliana] (Nucleic Acids Res. 27 (2), 470-478 (1999));supported by full-length cDNA: Ceres: 39877. 248528_at putative proteinsimilar to unknown protein At5g50760 −2.18 1.01 0.008566 0.918675(emb|CAB86483.1) 264788_at putative DnaJ protein; supported byfull-length At2g17880 −2.19 −1.25 0.011101 0.265694 cDNA: Ceres: 22711.253957_at putative protein; supported by cDNA: At4g26320 −2.19 −1.160.006508 0.414219 gi_10880502_gb_AF195894.1_AF195894 247199_at DNAbinding protein TGA1a homolog; supported At5g65210 −2.19 1.09 0.0100730.256741 by full-length cDNA: Ceres: 31032. 247170_at putative proteincontains similarity to lectin-like At5g65530 −2.19 1.2 0.020752 0.326964protein kinase 250099_at unknown protein; supported by cDNA: At5g17300−2.2 1.13 0.018091 0.37707 gi_14190364_gb_AF378860.1_AF378860 247474_atputative protein predicted proteins, Arabidopsis At5g62280 −2.21 −1.010.016382 0.887761 thaliana 261768_at gibberellin 3 beta-hydroxylase,putative similar to At1g15550 −2.22 1.01 0.037882 0.920313 gibberellin 3beta-hydroxylase GI: 3982753 from [Arabidopsis thaliana]; supported bycDNA: gi_1945343_gb_L37126.1_ATHGA4A 259264_at putative aldose1-epimerase shows similarity to At3g01260 −2.22 1.22 0.023126 0.227322aldose epimerases 253812_at putative wound induced protein wound-inducedAt4g28240 −2.25 −1.09 0.00548 0.137021 protein-tomato (fragment), PIR2:S19773; supported by full-length cDNA: Ceres: 20161. 246917_atserine-rich protein; supported by full-length cDNA: At5g25280 −2.25 1.240.008947 0.039883 Ceres: 99323. 261265_at hypothetical protein predictedby At1g26800 −2.26 1.2 0.022793 0.218643 genscan+; supported byfull-length cDNA: Ceres: 250127. 246229_at pectinesterase like proteinAt4g37160 −2.26 1.07 0.01383 0.725863 250012_x_at auxin-inducedprotein-like At5g18060 −2.27 1.11 0.022574 0.446969 259751_at putativetranscription factor similar to myb-related At1g71030 −2.29 −1.310.004307 0.051811 transcription factor 24 GB: S71287; supported by full-length cDNA: Ceres: 31592. 246932_at ethylene-responsive element-likeprotein ethylene- At5g25190 −2.31 −1.28 0.015246 0.042175 responsiveelement binding protein homolog, Stylosanthes hamata, EMBL: U91857;supported by cDNA: gi_15010715_gb_AY045659.1_(—) 264463_at unknownprotein similar to ESTs gb|T20511, At1g10150 −2.32 −1.04 0.0074280.701582 gb|T45308, gb|H36493, and gb|AA651176; supported by full-lengthcDNA: Ceres: 2558. 252178_at putative protein various predicted proteinsAt3g50750 −2.33 1.17 0.016542 0.191688 247149_at unknown protein;supported by full-length cDNA: At5g65660 −2.33 −1.03 0.011232 0.82378Ceres: 25419. 260855_at phosphatidylinositol-4-phosphate 5-kinase,putative At1g21920 −2.34 1.02 0.010684 0.812177 similar tophosphatidylinositol-4-phosphate 5-kinase GB: CAB53377 GI: 5777366 from[Arabidopsis thaliana]; supported by full-length cDNA: Ceres: 37462.256743_at Expressed protein; supported by full-length cDNA: At3g29370−2.34 1.09 0.007379 0.34665 Ceres: 22461. 249065_at putative proteinsimilar to unknown protein (gb At5g44260 −2.34 −1.05 0.002162 0.688129AAD10689.1); supported by cDNA: gi_14334449_gb_AY034916.1_(—) 264524_attat-binding protein, putative Highly Similar to At1g10070 −2.35 −1.060.006931 0.464612 branched-chain amino acid aminotransferase; Locationof EST gb|T44177 and gb|AA395381; supported by cDNA:gi_15293208_gb_AY051038.1_(—) 264521_at unknown protein Location of ESTgb|T41885 and At1g10020 −2.37 −1.37 0.002442 0.03961 gb|AA395021258091_at hypothetical protein predicted by genmark; supported At3g14560−2.37 1.27 0.014798 0.126209 by full-length cDNA: Ceres: 19279.261480_at phytochrome kinase substrate 1, putative similar to At1g14280−2.39 1.06 0.004881 0.498893 phytochrome kinase substrate 1 GI: 5020168from [Arabidopsis thaliana]; supported by full-length cDNA: Ceres:97569. 252040_at putative protein hypothetical protein F10M6.70-At3g52060 −2.39 −1.02 0.011127 0.860596 Arabidopsis thaliana, PIR3:T05399; supported by cDNA: gi_15293266_gb_AY051067.1_(—) 246001_atputative protein predicted protein, Arabidopsis At5g20790 −2.39 −1.630.007949 0.0182 thaliana; supported by full-length cDNA: Ceres: 267031.258809_at NAM-like protein (no apical meristem) similar to At3g04070−2.4 −1.24 0.010367 0.050869 NAM GB: CAA63101 [Petunia × hybrida]258362_at unknown protein At3g14280 −2.41 −1.2 0.007995 0.150833249467_at NAM/CUC2-like protein CUC2, Arabidopsis At5g39610 −2.41 −1.480.007479 0.036136 thaliana, EMBL: ATAB2560; supported by full- lengthcDNA: Ceres: 113779. 251665_at responce reactor 4; supported by cDNA:At3g57040 −2.42 −1.1 0.008685 0.45678 gi_3273201_dbj_AB010918.1_AB010918263382_at putative anthranilate N- At2g40230 −2.45 −1.06 0.0181350.712794 hydroxycinnamoyl/benzoyltransferase; supported by full-lengthcDNA: Ceres: 105546. 246071_at ids4-like protein ids-4 protein-Hordeumvulgare, At5g20150 −2.47 −1.14 0.002464 0.214703 PIR: T05905; supportedby full-length cDNA: Ceres: 32843. 247585_at putative protein predictedproteins, Arabidopsis At5g60680 −2.5 −1.09 0.002909 0.183267 thaliana;supported by full-length cDNA: Ceres: 16638. 264210_at putativemyb-related transcription factor Similar to At1g22640 −2.51 1.26 0.005620.068761 myb-related transcription factor (THM27) gb|X95296 from Solanumlycopersicum. ESTs gb|T42000, gb|T04118, gb|AA598042, gb|AA394757 andgb|AA598046 come from this gene; supported by cDNA: gi_3941409_gb_AF252965_at putative auxin-induced protein auxin-induced At4g38860 −2.53−1.12 0.006173 0.26078 protein 10A, Glycine max., PIR2: JQ1099 253814_atputative protein; supported by full-length cDNA: At4g28290 −2.55 −1.460.006294 0.044367 Ceres: 10077. 246523_at CONSTANS-like 1 At5g15850−2.55 1.01 0.013312 0.900077 263325_at putative RING zinc fingerprotein; supported by At2g04240 −2.56 1.18 0.004531 0.13068 cDNA:gi_13265496_gb_AF324691.2_AF324691 265342_at hypothetical proteinpredicted by genscan; supported At2g18300 −2.58 1.1 0.014912 0.315678 bycDNA: gi_15724317_gb_AF412099.1_AF412099 253872_at putative proteinArabidopsis thaliana nap At4g27410 −2.58 1.21 0.004591 0.057522 gene,PID: e1234813; supported by full-length cDNA: Ceres: 38344. 264783_atputative calcium-dependent protein kinase (U90439) At1g08650 −2.6 −1.610.010263 0.046318 similar to ESTs gb|T46119, gb|H76837, and gb|H36948;supported by cDNA: gi_6318612_gb_AF162660.1_AF162660 266363_athypothetical protein predicted by genscan and At2g41250 −2.64 −1.630.002674 0.015646 genefinder 260070_at putative helix-loop-helixDNA-binding protein At1g73830 −2.64 −1.19 0.010198 0.127406 containsPfam profile: PF00010 Helix-loop-helix DNA-binding domain 250844_atputative protein; supported by full-length cDNA: At5g04470 −2.64 1.220.009233 0.425631 Ceres: 13812. 256589_at cytochrome P450, putativecontains Pfam profile: At3g28740 −2.66 −1.69 0.010428 0.037959 PF00067cytochrome P450; supported by cDNA: gi_15292830_gb_AY050849.1_(—)265067_at hypothetical protein predicted by At1g03850 −2.7 1.37 0.0041240.138732 genefinder; supported by full-length cDNA: Ceres: 271253.256914_at hypothetical protein At3g23880 −2.72 1.01 0.02091 0.915885251169_at putative protein putative protein At2g25690- At3g63210 −2.731.13 0.005839 0.38507 Arabidopsis thaliana, EMBL: AC006053; supported byfull-length cDNA: Ceres: 40080. 255934_at cytochrome P450, putativesimilar to cytochrome At1g12740 −2.74 −1.11 0.010048 0.828407 P450 GI:4176420 from [Arabidopsis thaliana] 266150_s_at hypothetical proteinAt2g12290 −2.77 1.08 0.009686 0.668542 259502_at unknown protein;supported by cDNA: At1g15670 −2.77 −1.23 0.002226 0.019701gi_15146331_gb_AY049307.1_(—) 263283_at hypothetical protein predictedby genscan and At2g36090 −2.79 1.26 0.004 0.034558 genefinder 253125_atDnaJ-like protein DnaJ-like protein, Phaseolus At4g36040 −2.83 1.30.002096 0.029069 vulgaris, PATX: G1684851 248208_at unknown proteinAt5g53980 −2.83 −1.12 0.002744 0.19142 264021_at putativeauxin-regulated protein; supported by full- At2g21200 −2.85 1.14 0.011160.255677 length cDNA: Ceres: 7141. 249755_at unknown protein; supportedby full-length cDNA: At5g24580 −2.87 −1.02 0.01127 0.906115 Ceres: 6393.255284_at 5-adenylylsulfate reductase; supported by full- At4g04610 −2.9−1.53 0.007861 0.08308 length cDNA: Ceres: 40330. 253207_at putativeprotein small auxin up-regulated RNA, At4g34770 −2.9 −1.24 0.0048420.041275 Malus domestica, gb: Z93766 252118_at putative protein variouspredicted proteins, At3g51400 −2.9 −1.18 0.019242 0.328518 Arabidopsisthaliana; supported by full-length cDNA: Ceres: 14797. 247540_atethylene responsive element binding factor-like At5g61590 −2.99 1.030.003616 0.728822 ethylene responsive element binding factor 5,Arabidopsis thaliana, SWISSPROT: ERF5_ARATH; supported by full- lengthcDNA: Ceres: 19893. 264379_at hypothetical protein predicted by grailAt2g25200 −3 −1.3 0.023213 0.145635 263688_at unknown protein Locationof EST 228A16T7A, At1g26920 −3.05 −1.22 0.00728 0.304232 gb|N65686;supported by full-length cDNA: Ceres: 24946. 246522_at bZIP DNA-bindingprotein-like putative bZIP At5g15830 −3.09 −1.46 0.010759 0.157233DNA-binding protein-Capsicum chinense, EMBL: AF127797 258059_at NAM-likeprotein (No Apical Meristem) similar to At3g29035 −3.25 1.32 0.0044730.140279 GB: CAA63101 from [Petunia × hybrida] (Cell 85 (2), 159-170(1996)) 259982_at putative RING zinc finger protein contains PfamAt1g76410 −3.31 −1.01 0.011262 0.945494 profile: PF00097 Zinc finger,C3HC4 type (RING finger); supported by full-length cDNA: Ceres: 27464.262986_at unknown protein similar to hypothetical protein At1g23390−3.44 −1.22 0.008132 0.177105 GB: AAF27090 GI: 6730669 from (Arabidopsisthaliana); supported by full-length cDNA: Ceres: 101865. 260287_atunknown protein contains two Kelch motifs; At1g80440 −3.57 −1.180.008035 0.221837 supported by full-length cDNA: Ceres: 32885. 247754_atputative protein At5g59080 −3.77 −1.55 0.004279 0.021198 267238_atunknown protein; supported by full-length cDNA: At2g44130 −3.86 1.180.003036 0.152629 Ceres: 6950. 266156_at hypothetical protein predictedby genscan At2g28110 −3.99 1.1 0.004914 0.561885 266322_at putativeauxin-regulated protein At2g46690 −4 −1.09 0.003394 0.327782 258367_atputative protein kinase similar to protein kinase At3g14370 −4.02 −1.070.005242 0.532182 homolog GB: AAC78477 from [Arabidopsis thaliana];supported by full-length cDNA: Ceres: 96699. 253155_at putative proteinpredicted protein, Arabidopsis At4g35720 −4.2 −1.28 0.00697 0.318015thaliana 265573_at putative zinc-finger protein similar to zinc-fingerAt2g28200 −4.25 −1.33 0.00752 0.040354 protein GB: AAC98446 247696_atMYB27 protein-like MYB27 protein, Arabidopsis At5g59780 −4.32 1.370.003111 0.017905 thaliana, PIR: T46166; supported by cDNA:gi_3941479_gb_AF062894.1_AF062894 250937_at putative protein variouspredicted proteins, At5g03230 −4.33 1.47 0.010367 0.036447 Arabidopsisthaliana; supported by cDNA: gi_13878024_gb_AF370275.1_AF370275251443_at putative protein unknown protein At2g44130- At3g59940 −4.721.12 0.001814 0.186012 Arabidopsis thaliana, EMBL: AC004005; supportedby full-length cDNA: Ceres: 8014. 261177_at hypothetical proteinpredicted by genemark.hmm At1g04770 −5.29 −1.41 0.001922 0.031579249454_at expressed protein predicted protein, Synechocystis At5g39520−5.74 −1.29 0.003609 0.135283 sp., PIR: S77152; supported by full-lengthcDNA: Ceres: 5331. 265387_at unknown protein; supported by full-lengthcDNA: At2g20670 −6.17 −1.57 0.002564 0.056602 Ceres: 34827. 254265_s_atserine threonine kinase-like protein KI domain At4g23140 2.94 1.760.151164 0.015078 interacting kinase 1 (KIK1), Zea mays; supported bycDNA: gi_13506746_gb_AF224706.1_AF224706 263539_at putative tyrosineaminotransferase; supported by At2g24850 2.01 2.2 0.066727 0.012756full-length cDNA: Ceres: 14570. 265837_at unknown protein At2g14560 1.912.1 0.278938 0.013727 263402_at hypothetical protein similar tohypothetical protein At2g04050 1.65 1.87 0.126971 0.028665 GB: AAC27412256766_at Expressed protein; supported by cDNA: At3g22231 1.62 1.870.168568 0.005967 gi_14335055_gb_AY037207.1_(—) 263061_at putativeAAA-type ATPase At2g18190 1.48 1.94 0.324983 0.049719 267024_s_atputative aquaporin (plasma membrane intrinsic At2g34390 1.46 1.990.056378 0.04848 protein) 245035_at unknown protein similar to At2g264001.39 1.78 0.302025 0.044811 GP|2244827|gnl|PID|e326818|Z97336 252746_atsucrose synthase-like protein SUCROSE At3g43190 1.35 2.67 0.113720.012763 SYNTHASE (SUCROSE-UDP GLUCOSYLTRANSFERASE), Arabidopsisthalina, SWISSPROT: SUS1_ARATH; supported by cDNA:gi_14334569_gb_AY034958.1_(—) 263401_at hypothetical protein similar tohypothetical protein At2g04070 1.22 2.22 0.734988 0.005027 GB: AAC27412245306_at Expressed protein; supported by full-length cDNA: At4g146901.2 2.16 0.22188 0.009285 Ceres: 95834. 258277_at putative cytochromeP450 similar to cytochrome At3g26830 1.04 2.61 0.754479 0.013858 P45071B2 GB: O65788 [Arabidopsis thaliana] 252882_at Expressed protein;supported by full-length cDNA: At4g39675 −1.17 1.94 0.106839 0.012488Ceres: 14423. 261913_at flavin-containing monooxygenase FMO3, putativeAt1g65860 −1.63 −1.85 0.058793 0.008577 similar to flavin-containingmonooxygenase FMO3 GI: 349533 from [Oryctolagus cuniculus] 249727_atputative protein similar to unknown protein At5g35490 −1.2 −2.090.190584 0.008082 (gb|AAB61527.1) 254474_at putative protein predictedproteins, Arabidopsis At4g20390 −1.06 −1.71 0.572517 0.017439 thaliana;supported by full-length cDNA: Ceres: 248721. 260856_at TINY-likeprotein similar to TINY GB: CAA64359 At1g21910 1.17 −2.2 0.2681160.009082 GI: 1246403 from [Arabidopsis thaliana]; supported byfull-length cDNA: Ceres: 19721. 249215_at dihydroflavonol 4-reductaseAt5g42800 1.61 −1.77 0.401965 0.048093 254283_s_at anthocyanidinsynthase-like protein putative At4g22870 2.09 −1.98 0.161214 0.018458leucoanthocyanidin dioxygenase, Arabidopsis thaliana, PID: g1575699

TABLE 4 Genes that are Responsive to chitooctaose in the AtLysM RLK1mutant WT Mu Probe set Annotation Accession FC FC WT P Mu P 253046_atcytochrome P450 - like protein cytochrome P450, At4g37370 3.83 2.170.019261 0.016853 Glycyrrhiza echinata, AB001379; supported by full-length cDNA: Ceres: 253698. 254869_at protein kinase - like protein KIdomain interacting At4g11890 3.37 2.12 0.007665 0.003284 kinase 1 -Zeamays, PIR2: T02053 246099_at blue copper binding protein; supported byfull- At5g20230 2.67 1.7 0.008061 0.011289 length cDNA: Ceres: 7767.253317_at putative protein At4g33960 −1.83 −1.77 0.010341 0.022397260126_at putative hydroxymethyltransferase similar to serine At1g36370−1.93 −1.86 0.005701 0.006964 hydroxymethyltransferage GB: P50433 from[Solanum tuberosum]; supported by full-length cDNA: Ceres: 122515.246926_at putative protein At5g25240 −2.09 −2.21 0.019603 0.017979258217_at unknown protein contains Pfam profile PF00398 At3g17990 −2.21−2.27 0.009887 0.0037 Ribosomal RNA adenine dimethylases 258218_atmethyltransferase, putative similar to At3g18000 −2.21 −2.29 0.006670.009294 methyltransferase GB: AAC01738 from [Amycolatopsismediterranei] 254343_at PRH26 protein; supported by full-length cDNA:At4g21990 −2.22 −1.83 0.012838 0.031291 Ceres: 36866. 265121_at similarto flavin-containing monooxygenase At1g62560 −2.37 −1.87 0.0201260.00922 (sp|P36366); similar to ESTs gb|R30018, gb|H36886, gb|N37822,and gb|T88100 similar to flavin- containing monooxygenase GB: AAA21178GI:349534 from [Oryctolagus cuniculus]; supported by cDNA:gi_13877746_gb_AF37013 251039_at putative protein hypothetical proteinAt5g02020 −3.73 −1.91 0.001899 0.021967 T6H20.90 - Arabidopsis thaliana,EMBL: AL096859; supported by cDNA: gi_16648747_gb_AY058150.1_(—)259015_at unknown protein similar to hypothetical protein At3g07350−3.79 −1.81 0.001762 0.010373 GB: AAC17612 [Arabidopsis thaliana];supported by full-length cDNA: Ceres: 251012. 248676_at putative proteinsimilar to unknown protein At5g48850 −5.55 −4.23 0.003428 0.003335(gb|AAC72543.1) 249752_at putative protein similar to unknown protein(emb At5g24660 −5.87 −2.27 0.002654 0.005949 CAB62461.1); supported byfull-length cDNA: Ceres: 268701. 254265_s_at serine threonine kinase -like protein KI domain At4g23140 2.94 1.76 0.151164 0.015078 interactingkinase 1 (KIK1), Zea mays; supported by cDNA:gi_13506746_gb_AF224706.1_AF224706 263539_at putative tyrosineaminotransferase; supported by At2g24850 2.01 2.2 0.066727 0.012756full-length cDNA: Ceres: 14570. 265837_at unknown protein At2g14560 1.912.1 0.278938 0.013727 263402_at hypothetical protein similar tohypothetical protein At2g04050 1.65 1.87 0.126971 0.028665 GB: AAC27412256766_at Expressed protein; supported by cDNA: At3g22231 1.62 1.870.168568 0.005967 gi_14335055_gb_AY037207.1_(—) 263061_at putativeAAA-type ATPase At2g18190 1.48 1.94 0.324983 0.049719 267024_s_atputative aquaporin (plasma membrane intrinsic At2g34390 1.46 1.990.056378 0.04848 protein) 245035_at unknown protein similar to At2g264001.39 1.78 0.302025 0.044811 GP|2244827|gnl|PID|e326818|Z97336 252746_atsucrose synthase -like protein SUCROSE At3g43190 1.35 2.67 0.113720.012763 SYNTHASE (SUCROSE-UDP GLUCOSYLTRANSFERASE), Arabidopsisthalina, SWISSPROT: SUS1_ARATH; supported by cDNA:gi_14334569_gb_AY034958.1_(—) 263401_at hypothetical protein similar tohypothetical protein At2g04070 1.22 2.22 0.734988 0.005027 GB: AAC27412245306_at Expressed protein; supported by full-length cDNA: At4g146901.2 2.16 0.22188 0.009285 Ceres: 95834. 261913_at flavin-containingmonooxygenase FMO3, putative At1g65860 −1.63 −1.85 0.058793 0.008577similar to flavin-containing monooxygenase FMO3 GI:349533 from[Oryctolagus cuniculus] 249727_at putative protein similar to unknownprotein At5g35490 −1.2 −2.09 0.190584 0.008082 (gb|AAB61527.1) 258277_atputative cytochrome P450 similar to cytochrome At3g26830 1.04 2.610.754479 0.013858 P450 71B2 GB: O65788 [Arabidopsis thaliana] 252882_atExpressed protein; supported by full-length cDNA: At4g39675 −1.17 1.940.106839 0.012488 Ceres: 14423. 254474_at putative protein predictedproteins, Arabidopsis At4g20390 −1.06 −1.71 0.572517 0.017439 thaliana;supported by full-length cDNA: Ceres: 248721. 260856_at TINY-likeprotein similar to TINY GB: CAA64359 At1g21910 1.17 −2.2 0.2681160.009082 GI:1246403 from [Arabidopsis thaliana]; supported byfull-length cDNA: Ceres: 19721. 249215_at dihydroflavonol 4-reductaseAt5g42800 1.61 −1.77 0.401965 0.048093 254283_s_at anthocyanidinsynthase - like protein putative At4g22870 2.09 −1.98 0.161214 0.018458leucoanthocyanidin dioxygenase, Arabidopsis thaliana, PID: g1575699

The similar regulation patterns for this small number of genes in boththe mutant and wild-type plants may be due to some redundant functionprovided by one of the other four LysM RLKs in the mutant. Eventually,only 6 genes appeared to behave differentially in both the mutant andwild-type (last 6 rows in Table 4). The cause of such a discrepancy isnot clear. Since these few genes were only weakly to moderatelyregulated (−1.7 to 2.6 fold), experimental variation is a possiblecause.

To determine the functional classification of the 909 genes describedabove, information of these genes were input into the TAIR web-based GOannotation software. The output shows that the CRGs disclosed hereinclude many defense-related genes (such as genes encodingpathogenesis-related proteins and disease resistance proteins) andsignal transduction-related genes (such as various kinases andtranscription factors) (FIG. 12), suggesting a potential relationshipbetween gene induction and plant defense mediated bychitooligosaccharides.

Since the mutation in the AtLysM RLK1 gene blocked the regulation ofalmost all CRGs (˜98%) by the chitooligosaccharide, AtLysM RLK1 is verylikely the chitin receptor (or part of the receptor complex) that isresponsible for perceiving the chitooligosaccharide elicitor andinitiating cellular signaling leading to downstream gene expression.This notion is also indirectly supported by its structural features andthe findings that LysM RLKs NFR1 and NFR5 in the legume Lotus japonicusserve as the receptors for the lipo-chitin Nod signal. See Limpens etal., 2003; Madsen et al., 2003; Radutoiu et al., 2003.

Because many receptor kinases form heterodimers, it has been suggestedthat the legume NFR1 and NFR5 may function as a heterodimer complex. Seee.g., Goring et al., 2004. It is likely that AtLysRLK1 may require apartner protein, either another LysM RLK or a protein similar to therice CEBiP. Kaku et al., 2006. However, since mutations in the otherfour AtLysM RLK genes had no obvious effect on the expression ofselected CRGs, it seems unlikely that the products of these four genesare essential for the receptor function. There are three CEBiP-likeproteins in Arabidopsis, which are encoded by At1g21880, At1g77630 andAt2g17120, respectively.

If chitooligosaccharide recognition is an integral part of the responsepathway by which plants defend against fungal pathogens, mutations inthe AtLysM RLK1 gene should affect plant resistance to fungal pathogens.To test this hypothesis, three week-old mutant and wild-type plants wereinoculated with the biotrophic powdery mildew fungal pathogen Erysiphecichoracearum. Ten days later, the mutant plants appeared to supportmore fungal growth than the wild-type plants.

The susceptibility appeared to be less than that observed in NahGplants, which express salicylate hydrolase, preventing the accumulationof salicylic acid, and are therefore very susceptible to the fungalpathogen (FIG. 13A). Trypan blue staining of the infected leaves alsoshowed the AtLysM RLK1 mutant supported more hyphal growth andproduction of conidiophores earlier than the wild-type plants (FIG.13B). Arrows indicate sites where conidiophores are forming. Allphotographs were taken six days after inoculation. Bar=0.1 mm 4-week-oldplants were also inoculated with the necrotrophic fungus Alternariabrassicicola. Three days after inoculation, the mutant developedslightly bigger lesions than the wild-type plants, as measured byaverage diameter of the lesions (FIGS. 13C and 13D). In agreement withthis, the mutant plants also produced more spores per lesion than thewild-type plants (FIG. 13E).

To test the specificity of AtLysM RLK1 in fungal disease resistance, theresponse of the mutant to the bacterial pathogen Pseudomonas syringaepv. Tomato DC3000 was also examined. After infiltration with thepathogen, both the mutant and wild-type plants supported a similarbacterial growth three days after inoculation (FIG. 13F), indicatingthat defense against bacterial infection was not affected by themutation. WT=wild-type Col-0; Mu=the AtLysM RLK1 mutant. CSC=crab shellchitin, 8mer=chitooctaose, and water=distilled water. Empty columns=WTCol-0 and solid black columns=the AtLysM RLK1 mutant. Asterisks indicatestatistically significant differences between the mutant and wild-typeplants (P<0.05). Error bars=standard error. Each experiment was repeatedat least twice with similar results.

The mutation in the AtLysM RLK1 gene led to only moderate susceptibilityto fungal pathogens, suggesting that AtLysM RLK1 plays a role inmediating basal or general resistance to fungal pathogens through therecognition of the chitooligosaccharide PAMP derived from fungal cellwalls. This result is not surprising because it is well documented thatfungal pathogens produce multiple elicitors that induce plant innateimmunity. See e.g., Chisholm et al., 2006. Thus, blocking the chitinresponse pathway would not be expected to completely block all defenseresponses mounted by the plant against the fungal pathogen.

This notion is supported by the observation that chitin-responsivedefense genes (e.g., MPK3 and WRKY53) were still induced by the fungalpathogen A. brassicicola in the mutant, albeit to a lower level comparedwith that in wild-type plants (FIG. 14). The gene induction by thefungal pathogen is monitored by quantitative RT-PCR at different timepoints after inoculation. Each data point is the average of the relativegene expression (fold change, normalized to actin-2 and relative to thetime 0 sample) from three replicates. Error bar=standard error.WT=wild-type Col-0; Mu=the AtLysM RLK1 mutant. This low level expressionof some defense genes in the mutant may explain why the mutant was onlymoderately susceptible to the fungal pathogens as compared to thewild-type plants.

Pretreatment of rice plants by chitooligosaccharide has been shown toenhance fungal resistance in rice. Tanabe et al., 2006. It is shown herethat pretreatment of wild-type plants with chitooligosaccharides reduceddisease symptoms upon inoculation with the fungal pathogen A.brassicicola, as evidenced by reduced lesion size and spore production(FIGS. 13C, 13D and 13E). Pretreatment also inhibited the growth of thebacterial pathogen P. syringae pv. tomato DC3000 (FIG. 13F), reflectinga general induction of plant innate immunity. In contrast, similarpretreatment of the AtLysM RLK1 mutant plants did not enhanceresistance. These data further support the critical role for AtLysM RLK1in mediating the perception of chitooligosaccharides by plants.

Chitin is present in the cell walls of all true fungi, but not inplants. Fungal pathogens with defects in chitin synthesis aresignificantly less virulent on susceptible hosts, including both plantsand animals. See Bulawa et al., 1995; and Soulie et al., 2006. Asdisclosed herein, AtLysM RLK1 is likely a receptor for chitin PAMP offungal pathogen. AtLysM RLK1 is only the third pattern recognitionreceptor (PRR) identified in plants. The other two PRRs are bothleucine-rich repeat receptor-like kinases (LRR RLKs). Nürnberger et al.,2006. Therefore, this finding adds a new class of proteins to the familyof plant PRRs.

LysM RLK NFR1 and NFR5 Nod signal receptors specifically recognize alipochitin molecule with a back-bone of 4-5 units ofN-acetyl-D-glucosamine. For review, see Stacey et al. 2006. Thisspecificity is supported by the findings that mutations in either of theNFR1 and NFR5 genes in L. japonicus did not block the induction of theselected CRGs in this plant (FIG. 15). In more details, both the wildtype (Gifu) and the Nod signal receptor mutants nfr1-1 and nfr5-1 weretreated with chitooctaose for 30 minutes at a concentration of 1 μM orwith water (as a control). The selected CRGS were detected usingsemi-quantitative RT-PCR. LjActin-2 was used as an internal control.

However, previous results suggested that both the legume NFR genes andAtLysM RLK1 are under negative selection, implying the functionalconservation between legume NFR and AtLysM RLK1 genes. Zhang et al.,2007. Perhaps, the discrepancy in substrate specificity lies in thedifference in their extracellular LysM domains, since legume NFRproteins have two LysM motifs while AtLysM RLK1 has three. Zhang et al.,2007.

To determine whether the AtLysM RLK1 mutation affects otherdefense-related pathways, such as the salicylic acid (SA) and jasmonicacid/ethylene (JA/ETH) responsive pathways, the AtLysM RLK1 mutant andwild-type plants were treated with SA, methyl jasmonic acid (MeJA), and1-aminocyclopropane-1-carboxylic acid (ACC), respectively, andexpression of the pathway hallmark genes, PR-1 (the SA pathway) andPDF1.2 (the JA/ETH pathway) was examined.

Quantitative RT-PCR data demonstrated that both the mutant and wild-typeplants showed similar induction of PR-1 by SA and of PDF1.2 by MeJA orACC, indicating that the mutation did not affect these defense pathways(FIG. 16). In addition, the mutant plants were fully responsive toanother typical PAMP, the flagellin-derived peptide flg22 (FIG. 16).Each data point is the average of the relative gene expression (foldchange, normalized to actin-2 and relative to the control sample) fromthree replicates. Error bar=standard error. No statistically significantdifferences are found between the mutant and wild type in the inductionof the above genes.

Interestingly, as shown by FIG. 17, the AtLysM RLK1 mutation does notblock the induction of flagellin-responsive genes. Collectively, thedata indicate that AtLysM RLK1 is the primary, specific receptor forrecognition of the chitooligosaccharide PAMP derived from fungalpathogen cell walls. This recognition is a crucial step in theelicitation of protective innate immunity responses in the plant.

Example 4 Forced Expression of Certain LysM RLK Genes Enhanced FungalResistance in Plants

Over-expression of one LysM RLK gene, At2g33580, under a strongcauliflower mosaic virus (CMV) 35S promoter in transgenic plants,resulted in enhanced disease resistance. Therefore, this gene mayfunction in a positive way to elevate disease resistance, similar to themechanism of the At3g21630 gene, as shown in FIG. 5. Together with thedata in Example 3 showing that forced expression of AtLysM RLK1 gene canrestore induction of CRGs in a AtLysM RLK1 insertion mutant, these dataconfirm that the expression of specific LysM RLK genes in transgenicplants may confer enhanced disease resistance.

Example 5 Induction of Gene Expression by Chitin or its Derivatives

Based on the genome-wide gene expression studies using microarrays,quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR)was conducted to identify over 120 different transcription factors inArabidopsis thaliana whose expression is enhanced by chitin treatment.Many of these transcription factors are known to be involved in fungalpathogen response. This again shows the correlation of chitin responseto disease resistance. Each of these transcription factors is apotential target for genetic manipulation in order to enhance diseaseresistance. The results of this study are described in greater detailsin Libault et al., 2007, which is hereby expressly incorporated byreference.

Some of the genes disclosed herein, including the LysM RLK genes, theCRGs such as the transcription factors described above, may play apositive role in plant fungal defense. Such genes may be called positiveregulators. Transgenic plants may be generated wherein these positiveregulators are expressed at an elevated level to increase the expressionof transcription factors or other downstream genes. Some of the genes,on the other hand, may inhibit a plant's fungal defense capability. Suchgenes may be called negative regulators (also called “negativeregulatory genes”). Deletion mutants of such genes that play a negativerole in fungal defense may be created to obtain plants with enhancedfungal defense capability. Alternatively, dominant negative mutants ofthe negative regulatory genes may be introduced into a wild-type plantto inhibit the function of negative factors. Host plants may include anyplants that may be susceptible to fungal infection, such as Arabidopsisthaliana, soybean, and others.

Example 6 LysM Containing Proteins in Soybean

Utilizing the gene sequences from Arabidopsis, as described above, atotal of 13 LysM RLK genes were identified in the soybean genome bysearching the dbEST sequence database maintained by the Institute ofGenomic Research. These 13 soybean LysM RLKs are: GmNFR1α (also referredto as GmNFR1a in this disclosure), GmNFR1β (also referred to as GmNFR1bin this disclosure), GmLYK2, GmLYK3, GmLYK4 (previously known asGmLysM17), GmNFR5α (also referred to as GmNFR5a in this disclosure),GmNFR5β (also referred to as GmNFR1b in this disclosure), GmLYK6(previously known as GmLysM14), GmLYK7, GmLYK8 (previously known asGmLysM4), GmLYK9 (previously known as GmLysM16), GmLYK10, GmLYK11, andare designated as SEQ ID Nos. 54-66, respectively.

In addition, an additional fifteen soybean genes were identified thatappear to have a LysM domain, but no associated kinase domain. PCRprimers were developed for several of these genes, and their location onthe soybean bacterial artificial chromosome (BAC)-based physical map wasdetermined by probing pools of individual BAC clones. In this way, BACclones encoding the various LysM domain proteins were identified. Atthis time, twelve BACs have been sequenced and the genomic sequences,including the regulatory regions, have been obtained for several LysMRLK genes.

Sequence comparisons between the soybean BAC sequences and other plantspecies showed examples where gene order (microsynteny) was wellconserved. For example, FIG. 18 shows microsynteny between the soybeanGmNFR5 and LysM17 (GmLYK4) gene-encoding regions and correspondingregions in poplar (Pt), Lotus japonicus (Lj), and Medicago trancatula(Mt) Arabidopsis thaliana (At) and rice (Os). These regions ofmicrosynteny may be expanded by use of these methods to other plantspecies. Thus, knowledge of the genomic location in soybean can allowfor the identification of the likely functional orthologue in otherplant species, or vice versa.

In some cases, mapping the gene to the physical map also gave a geneticmap location, due to genetic markers associated with the BAC clones.Table 5 shows examples of such regions that are in proximity to LysM RLKencoding regions. The locations of these genes were correlated withknown quantitative trait loci (QTLs) associated with fungal resistance,i.e., Sclerotina white mold, Asian soybean rust and sudden deathsyndrome. In each case, a close correlation existed between the locationof the LysM RLK and a known QTL for disease resistance. Thus, mapping ofthe LysM RLK may aid in the localization of disease resistance QTLs insoybean. The sequence of the LysM RLK gene can also be used to definebetter genetic markers for fine mapping of the associated QTLs. Forinstance, soybean mutants may be generated and selected for fungalresistant phenotypes. The close genetic link between certain QTLs andsome LysM RLK genes may allow one to use the LysM RLK gene sequences totrace segregation of the QTLs. For example, molecular markers in theform of PCR primers, oligonucleotide probes, single nucleotidepolymorphisms, restriction fragment polymorphisms, among others, derivedfrom the DNA sequence of the LYK genes could be very useful in followinga specific QTL in a breeding process.

TABLE 5 Associations of GmLysM-RLKs with known fungal resistance QTLsGenetic Genetic Linkage position Soybean LysM-RLKs marker Group (cM)Sclerotinia sclerotiorum QTL Satt172 D1b 100.89 Sclerotinia sclerotiorumQTL Satt459 D1b 118.62 K411_1 D1b 119.34 GmLysM4, GmLysM26, GmNFR1aA343_2 D1b 120.97 Sclerotinia sclerotiorum QTL Satt143 L 30.19 GmLysM23Sat_388 L 30.86 Sclerotinia sclerotiorum QTL Satt481 L 54.57 GmLysM25Sat_402 C2 103.33 Asian soybean rust QTL Satt460 C2 117.77 Fusariumsolani f. sp glycines (SDS) Satt307 C2 121.27 QTL

More particularly, all or a fragment of the polynucleotides of theinstant disclosure may be used as probes for genetically and physicallymapping the genes of which they are a part, and can be further used asmarkers for traits linked to those genes. Such information may be usefulin plant breeding in order to develop lines with desired phenotypes. Forexample, the instant nucleic acid fragments may be used as restrictionfragment length polymorphism (RFLP) markers. Southern blots ofrestriction-digested plant genomic DNA may be probed with the nucleicacid fragments of the instant disclosure. The resulting banding patternsmay then be subjected to genetic analyses using computer programs suchas MapMaker (Lander et al. (1987) Genomics 1:174-181) in order toconstruct a genetic map. In addition, the nucleic acid fragments of theinstant disclosure may be used to probe Southern blots containingrestriction endonuclease-treated genomic DNAs of a set of individualsrepresenting parent and progeny of a defined genetic cross. Segregationof the DNA polymorphisms is noted and used to calculate the position ofthe instant nucleic acid sequence in the genetic map previously obtainedusing this population (Botstein et al. (1980) Am. J. Hum. Genet.32:314-331).

The production and use of plant gene-derived probes for use in geneticmapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol.Reporter 4:37-41. Numerous publications describe genetic mapping ofspecific cDNA clones using the methodology outlined above or variationsthereof. For example, F2 intercross populations, backcross populations,randomly mated populations, near isogenic lines, and other sets ofindividuals may be used for mapping. Such methodologies are well knownto those skilled in the art.

Nucleic acid probes derived from the instant nucleic acid sequences mayalso be used for physical mapping (i.e., placement of sequences onphysical maps; see Hoheisel et al. In: Non mammalian Genomic Analysis: APractical Guide, Academic press 1996, pp. 319-346, and references citedtherein). In another embodiment, nucleic acid probes derived from theinstant nucleic acid sequences may be used in direct fluorescence insits hybridization (FISH) mapping (Trask (1991) Trends Genet.7:149-154). Although current methods of FISH mapping favor use of largeclones ranging from a few Kb to several hundred Kb; see Laan et al.(1995) Genome Res. 5:13-20), improvements in sensitivity may allowperformance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods of genetic andphysical mapping may be carried out using the nucleic acid sequences ofthe instant disclosure. Examples include allele-specific amplification(Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism ofPCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics16:325-332), allele-specific ligation (Landegren et al. (1988) Science241:1077-1080), nucleotide extension reactions (Sokolov (1990) NucleicAcid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat.Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic AcidRes. 17:6795-6807). For these methods, the sequence of a nucleic acidfragment is used to design and produce primer pairs for use in theamplification reaction or in primer extension reactions. The design ofsuch primers is well known to those skilled in the art. In methodsemploying PCR-based genetic mapping, it may be necessary to identify DNAsequence differences between the parents of the mapping cross in theregion corresponding to the instant nucleic acid sequence. This,however, is generally not necessary for mapping methods.

Soybean genotypes used for mapping of soybean QTLs for white moldresistance included Corsoy 79 and Dassel. As shown in FIG. 19, treatmentof leaves of these plants, as well as Williams 82 as a control, resultedin strong induction of three of the LysM RLK genes out of a total of sixsuch genes tested. These genes are, therefore, excellent targets forgenetic manipulation using the methods demonstrated in Arabidopsis tocreate soybean plants with decreased disease susceptibility. Finally, aswas the case with Arabidopsis, some of the soybean LysM RLK genes areinduced upon treatment of soybean with chitin, as confirmed by theresults shown in FIG. 20. Leaves were treated by spraying with chitin(100 μM)+0.2% Tween-20.

Example 7 Tissue Specific Expression of LysM-Containing Proteins inSoybean and Other Plants

Other experiments examined the expression of the various LysMdomain-containing genes under various conditions. For the six plantspecies in this study, tissue expression levels of LYK genes have onlybeen reported for M. truncatula (Limpens et al., 2003; Arrighi et al.,2006) and Arabidopsis. Therefore, LYK gene expression was measured usingquantitative reverse transcription (RT)-PCR in different tissues ofsoybean, M. truncatula, and rice plants.

More particularly, Soybean, M. truncatula, and rice plants were grown inthe greenhouse at 28° C. to 30° C. with a 16-h light/8-h dark cycle.Roots and vegetative tissues were sampled about 3 weeks after plantingand flowers were sampled about 3 months after planting. Total RNAs wereextracted using Trizol (Invitrogen) followed by Turbo DNase (Ambion)treatment to remove genomic DNA contamination. First-strand cDNAs weresynthesized using Moloney murine leukemia virus reverse transcriptase(Promega). Quantitative RT-PCR was performed using a 7500 real-time PCRsystem (Applied Biosystems) following standard procedures. The primersequences are listed in Table 6. q-RT-PCR of GmSubi2, MtActin2, OsEF1αare used to normalize the expression data of all of the other genes inthe respective species.

TABLE 6  Plant LYK primers for qRT-PCR (5′ to 3′ from left to right) SEQSEQ Genes Forward ID No. Reverse ID No. GmSubi2 AGCTATTCGCAGTTCCCAAAT 96CAGAGACGAACCTTGAGGAGA 97 GmNFR1a AAGAACATCCGTGGAAAGGTT 98AATGTTCCCACAAGACGAGTG 99 GmNFR1b TGACATATGCCAATCTCACCA 100GTGACATTAACCGTGGCATTT 101 GmLYK2 GATCCACAACAACGTCCAAAT 102ATGGAAGCAATATCCCAATCC 103 GmLYK3 TAACGGTGACGTTGATGTTCA 104GTTGTCGAGGTTGATTTCTCG 105 GmLYK4 AGATGTGCTTGTCCCACAAAG 106CAGAATCACCCCAGTTTACCA 107 GmNFR5a ACCGCTCTTTTGCCAATATCT 108AACGGGGTTTAAATCCATCAC 109 GmNFR5b CATGGCCAGAACTTTTACCAA 110GTTGTCATGGCTTTCCTACCA 111 GmLYK9 TGATCTCCTACGTCGTCCAAC 112GCGTCAATGATGGACTGTTCT 113 GmLYK10 CCTCTCTCTCCAACCTCACCT 114CTGATCCTGGGAGAGGAACTC 115 GmLYK11 TTCGGTTCCTGGTGAGTCTTA 116TCATGGGGTACATGAGCTTTC 117 MtActin2 TGGCATCACTCAGTACCTTTCAACAG 118ACCCAAAGCATCAAATAATAAGTCAACC 119 MtLYK1 CATGAGCATTCAGTGCCTGT 120TGCAGAATCAGTAAGCCTGGT 121 MtLYK3 TGCTAAGGGTTCAGCTGTTGGTA 122AAATGCCCTAGAAGTTTGTGGAAG 123 MtLYK4 CGCAAGATGGATGTGTATGC 124CATGGCTCTCGAACTCGTTT 125 MtLYK9 CACTCATATTCTTTTCTGCCACCCA 126TGCAATGGATTGAGGACTGGTGT 127 MtLYK10 GGAAATGGAGAAATGGCAAA 128CGCCTTGACCAAGAAACCTA 129 MtLYK11 GGCATTGATGGGTCAGAACT 130TGCAAAGAGGATCACACTGC 131 MtLYK12 CTCTTCTTCTTCTTCTTCGTCAGCA 132GGTATGCTTGGCATGTTTGAGTTT 133 MtLYK13 GGTTGTTCTCGGAATCTTCG 134ATGCATGTATTGCAGACCGA 135 OsEF1α TTTCACTCTTGGTGTGAAGCAGAT 136GACTTCCTTCACGATTTCATCGTAA 137 OsLYK1 ATGGCGATATGGGTGACATT 138TCCACATGGAAGGTGAATGA 139 OsLYK2 GTTCTTGCGTCTGGTGCTCT 140CTCCTTATCCGGAGCCAAC 141 OsLYK3 ATGGAGGAGGTGTTCGTCAC 142CCGAGGACCATAGAAGCTGA 143 OsLYK4 CATGGTCACCTACCTCGTCA 144TATGATGGAGCTCTCGGTGA 145 OsLYK5 GTTCATCGACAAACCGATCA 146TAATACGAGCTGCCGAGCTT 147 OsLYK6 GTGACGAGGAGAATGGAGGA 148CTCGATCAGCTTCACCATCA 149

The data agree well with previous results on MtLYK expression levels(Limpens et al., 2003; Arrighi et al., 2006). It was also found thatplant LYK expression was generally tissue specific and that most plantLYK genes were expressed predominantly in the root in soybean (FIG.21A), M. truncatula (FIG. 21B), rice (FIG. 21C), L. japonicus (Madsen etal., 2003; Radutoiu et al., 2003), and Arabidopsis, although a few geneswere expressed in stems and leaves. Expression levels of each LYK genewere displayed in artificial scales relative to particular housekeepinggenes. Data were collected from three biological replicates. Error barsrepresent SDs.

As predicted from their orthologous relationships (Zhang et al, 2007),GmNFR1, GmNFR1, MtLYK3, and LjNFR1 (Radutoiu et al., 2003) showedsimilar patterns of root-specific expression. Similarly, GmNFR5, GmNFR5,MtLYK13, OsLYK5, and LjNFR5 (Madsen et al., 2003) showed root-specificexpression. These results are reasonable, from a biological perspective,because these receptors need to efficiently contact Nod factors secretedby soilborne symbiotic bacteria.

Additionally, the following sets of orthologous genes also exhibitsimilar expression patterns: GmLYK4 and MtLYK12; GmLYK10 and AtLYK2;GmLYK8 (data not shown); and AtLYK5. Interestingly, several duplicatedgenes displayed different expression patterns. For example, GmLYK2 andMtLYK11 expression is dramatically different from duplicated partners,GmNFR1 and MtLYK10, respectively. MtLYK9, paralogous to MtLYK13, isexpressed differently from the latter. These data suggest the functionaldiversification of LYK genes after duplications.

In light of the detailed description of the invention and the examplespresented above, it can be appreciated that the several aspects of theinvention are achieved.

It is to be understood that the present invention has been described indetail by way of illustration and example in order to acquaint othersskilled in the art with the invention, its principles, and its practicalapplication. Particular formulations and processes of the presentinvention are not limited to the descriptions of the specificembodiments presented, but rather the descriptions and examples shouldbe viewed in terms of the claims that follow and their equivalents.While some of the examples and descriptions above include someconclusions about the way the invention may function, the inventors donot intend to be bound by those conclusions and functions, but put themforth only as possible explanations.

Moreover, while most of the examples provided use Arabidopsis or soybeanas the host plant, it is to be understood that the transgenic and plantbreeding procedures described herein are broadly applicable to otherplant species as well. These other plants may include but are notlimited to: Rice, Wheat, Barley, poplar, M. truncatula, L. japonicus andmany other crops, vegetables, and trees. Although transformation andbreeding procedures differ from one plant species to another, it iswithin the skills of an ordinary artisan to modify the teaching of thisdisclosure for use in other plants. The methodology for conferringfungal resistance upon a plant or for selecting for a fungal resistantplant may be applicable to a broad spectrum of fungi, such as Fusarium,Powdery mildew, and the variety of fungi that cause soybean rust, amongothers.

It is to be further understood that the specific embodiments of thepresent invention as set forth are not intended as being exhaustive orlimiting of the invention, and that many alternatives, modifications,and variations will be apparent to those of ordinary skill in the art inlight of the foregoing examples and detailed description. Accordingly,this invention is intended to embrace all such alternatives,modifications, and variations that fall within the spirit and scope ofthe following claims.

REFERENCES

Full citations of references that are not fully cited in the text arelisted below. All references, including those that are not listed belowbut are fully cited in the text, are hereby incorporated by reference tothe same extent as though fully disclosed herein:

-   1. Arrighi J, Bane A, Ben Amor B, Bersoult A, Soriano L, Mirabella    R, Carvalho-Niebel F, Journet E, Gherardi M, Huguet T, et al (2006)    The Medicago truncatula lysine motif-receptor-like kinase gene    family includes NFP and new nodule-expressed genes. Plant Physiol    142: 265-279.-   2. Bulawa, C. E., D. W. Miller, L. K. Henry, J. M. Becker, Proc.    Natl. Acad. Sci. U.S.A. 92, 10570-10574 (1995).-   3. Chisholm, S. T., G. Coaker, B. Day, B. J. Staskawicz, Cell 124,    803-814 (2006).-   4. Clamp M, Cuff J, Searle S M, Barton G J (2004) The Jalview Java    alignment editor. Bioinformatics 20: 426-427.-   5. Day, R. B. et al., Plant Physiol. 126, 1162-1173 (2001).-   6. Eddy S R (1998) Profile hidden Markov models. Bioinformatics 14:    755-763.-   7. Felsenstein J (2000) PHYLIP (Phylogeny Inference Package), Ed    3.6. University of Washington, Seattle.-   8. Gomez-Gomez, L., T. Boller, Mol. Cell 5, 1003-1011 (2000).-   9. D. R. Goring, J. C. Walker, Science 303, 1474-1475 (2004).-   10. Ito, Y., H. Kaku, N. Shibuya, Plant J. 12, 347-356 (1997).-   11. Joris, B., FEMS Microbiol. Lett. 70, 257-264 (1992).-   12. Kaku, H. et al., Proc. Natl. Acad. Sci. U.S.A. 103, 11086-11091    (2006).-   13. Limpens et al., Science 302, 630-633 (2003).-   14. Libault, M., J. Wan, T. Czechowski, M. Udvardi, G. Stacey, Mol.    Plant-Microbe Interact. (in press) (2007).-   15. Libault M, Wan J, Joshi T, Zhang X, Czechowski T, Xu D, Udvardi    M, Stacey G (2006) The regulation of Arabidopsis transcription    factor and ubiquitin-ligase genes by chitin allows the    identification of a G-box motif highly represented in their promoter    sequences. Plant Physiol. (submitted).-   16. Libault, M., J. Wan, T. Czechowski, M. Udvardi, and G. Stacey,    Identification of 118 Arabidopsis Transcription Factor and 30    Ubiquitin-Ligase Genes Responding to Chitin, a Plant-Defense    Elicitor. Molecular Plant-Microbe Interactions, Vol. 20, No. 8,    2007, pp. 900-911.-   17. Madsen, E B; Madsen, L H; Radutoiu, S; Olbryt, M; Rakwalska, M;    Szczyglowski, K; Sato, S; Kaneko, T; Tabata, S; Sandal, N;    Stougaard, J. 2003. A receptor kinase gene of the LysM type is    involved in legume perception of rhizobial signals. Nature 425    (6958): 637-640.-   18. Nürnberger, T., B. Kemmerling, Trends Plant Sci. 11, 519-522    (2006).-   19. Okada, M. and M. Matsumura, Y. Ito, N. Shibuya, Plant Cell    Physiol. 43, 505-512 (2002).-   20. Passarinho, P., S. C. de Vries, In: The Arabidopsis Book,    American Society of Plant Biologists (2002).-   21. Radutoiu, S; Madsen, L H; Madsen, E B; Felle, H H; Umehara, Y;    Gronlund, M; Sato, S; Nakamura, Y; Tabata, S; Sandal, N;    Stougaard, J. 2003. Plant recognition of symbiotic bacteria requires    two LysM receptor-like kinases. Nature 425 (6958): 585-592.-   22. Ramonell, K., B. Zhang, R. Ewing, Y. Chen, D. Xu, G. Stacey,    and S. Somerville. 2002 Microarray analysis of chitin elicitation in    Arabidopsis thaliana. Mol. Plant Pathol. 3 (1): 301-311.-   23. Ramonell K, Berrocal-Lobo M, Koh S, Wan J, Edwards H, Stacey G    and Somerville S. 2005. Loss-of-function mutations in four chitin    responsive genes show increased susceptibility to the powdery mildew    pathogen, Erysiphe cichoracearum. Plant Physiol. 138: 1027-1036-   24. Schmidt H A, Strimmer K, Vingron M, von Haeseler A (2002)    TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets    and parallel computing. Bioinformatics 18: 502-504.-   25. Shibuya, N., E. Minami, Physiol. Mol. Plant Pathol. 59, 223-233    (2001).-   26. Soulie, M. C. et al., Cell Microbiol. 8, 1310-1321 (2006).-   27. Stacey, G. and N. Shibuya. 1997. Chitin recognition in rice and    legumes. Plant and Soil 194: 161-169.-   28. G. Stacey, M. Libault, L. Brechenmacher, J. Wan, G. D. May,    Curr. Opin. Plant. Biol. 9, 110-121 (2006).-   29. Tanabe, S., et al., Biosci. Biotechnol. Biochem. 70, 1599-1605    (2006).-   30. Thompson J D, Gibson T J, Plewniak F, Jeanmougin F, Higgins D    G (1997) The Clustal-X windows interface-flexible strategies for    multiple sequence alignment aided by quality analysis tools. Nucleic    Acids Res 25: 4876-4882-   31. Wan, Jinrong, Shuqun Zhang, and Gary Stacey. 2004. Activation of    a potential mitogen-activated protein kinase pathway in Arabidopsis    by chitin. Mol. Plant Pathol. 5(1): 125-135.-   32. Yang Z (1997) PAML: a program package for phylogenetic analysis    by maximum likelihood. Comput Appl Biosci 13: 555-556.-   33. Zhang, B., K. Ramonell, S. Somerville, and G. Stacey. 2002.    Characterization of Early, Chitin-Induced Gene Expression in    Arabidopsis Mol. Plant-Microbe Int. 15: 963-970.-   34. Zhang, X.-C. et al., Plant Physiol. 144, 623-636 (2007).-   35. Zmasek C M, Eddy S R (2001) ATV: display and manipulation of    annotated phylogenetic trees. Bioinformatics 17: 383-384.

What is claimed is:
 1. A transgenic plant comprising a transgene, saidtransgene having substantial sequence similarity to a LysM receptorkinase family gene.
 2. The transgenic plant according to claim 1,wherein the LysM receptor kinase family gene is selected from the groupconsisting of polynucleotides of SEQ ID Nos. 1-2 and 4-6.
 3. Thetransgenic plant according to claim 1, wherein the LysM receptor kinasefamily gene has a coding sequence that is at least 95% identical to thecoding sequence of the polynucleotide of SEQ ID No.
 6. 4. The transgenicplant according to claim 1, wherein the LysM receptor kinase family geneis selected from the group consisting of polynucleotides of SEQ ID Nos.54-95.
 5. The transgenic plant according to claim 1, wherein the plantis soybean.
 6. The transgenic plant according to claim 1, wherein theplant is Arabidopsis thaliana.
 7. The transgenic plant according toclaim 1 wherein the LysM receptor kinase family gene encodes afunctional LysM receptor kinase.
 8. The transgenic plant according toclaim 1, further comprising at least one regulatory sequence operablylinked to said LysM receptor kinase family gene or fragment, saidregulatory sequence controlling the expression level of the LysMreceptor kinase family gene or fragment.
 9. A plant comprising a LysMreceptor kinase family gene having at least one mutation, said mutatedgene being derived from an endogenous LysM receptor kinase family gene.10. The plant of claim 9, wherein the mutated LysM receptor kinasefamily gene encodes a LysM receptor kinase with a mutation selected fromthe group consisting of amino acid substitution, deletion and insertion.11. The plant of claim 9, wherein the mutation of the LysM receptorkinase family gene alters the expression level of the encoded LysMreceptor kinase in said plant.
 12. A method for protecting a plant fromfungal infection, comprising the step of introducing into said plant atransgene, said transgene having substantial sequence similarity to aLysM receptor kinase family gene or fragment thereof.
 13. The method ofclaim 12, further comprising the step of expressing a LysM receptorkinase encoded by said transgene.
 14. The method of claim 12, whereinthe LysM receptor kinase family gene is selected from the groupconsisting of polynucleotides of SEQ ID Nos. 1-2 and 4-6.
 15. The methodof claim 12, wherein the LysM receptor kinase family gene has a codingsequence that is at least 95% identical to the coding sequence of thepolynucleotide of SEQ ID No.
 6. 16. The method of claim 12, wherein theLysM receptor kinase family gene is selected from the group consistingof polynucleotides of SEQ ID Nos. 54-95.
 17. A method for preventingfungal infection, comprising the step of generating the plant of claim9.
 18. The method according to claim 17 wherein the plant is soybean.19. The method according to claim 17 wherein the plant is Arabidopsisthaliana.
 20. The method of claim 17, wherein the LysM receptor kinasefamily gene is selected from the group consisting of polynucleotides ofSEQ ID Nos. 1-2, 4-6 and 54-95.